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This page lists the software packages that are installed on Argon. Note that combining our HPC systems, and making Argon "live forever", necessitated some changes in how the software is managed. Previously, the stack would be viable for the life of a cluster system but that is no longer feasible given the long lived nature of Argon. In the new HPC model there needs to be a way to update all levels of the software stack while maintaining a consistent set of dependencies, while still maintaining older versions of software should they be needed. This is accomplished by updating the entire stack of software but maintaining the previous stack as well. One extra level of the environment module hierarchy was introduced to manage this, with a versioned "stack" module. The original set of packages will be maintained and for now is always visible. The newer sets of packages are made visible by loading a "stack" module. 

For instance, given default module set when logging in, the version of bcftools is 1.3.1.

$ module avail bcftools


----------------------------------------------------- /opt/modules -----------------------------------------------------
   bcftools/1.3.1


Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

However, there are newer versions available via the "stack" modules. All modules can be seen with the module spider command.

$ module spider bcftools


--------------------------------------------------------------------------------------------------------------------
  bcftools:
--------------------------------------------------------------------------------------------------------------------
     Versions:
        bcftools/1.3.1
        bcftools/1.9_gcc-4.9.4
        bcftools/1.9_gcc-9.1.0
        bcftools/1.10.2_gcc-4.9.4
        bcftools/1.10.2_gcc-8.3.0
        bcftools/1.10.2_gcc-9.2.0
        bcftools/1.10.2_intel-19.0.5.281


--------------------------------------------------------------------------------------------------------------------
  For detailed information about a specific "bcftools" module (including how to load the modules) use the module's full 
name.
  For example:


     $ module spider bcftools/1.9_gcc-9.1.0
--------------------------------------------------------------------------------------------------------------------

 Following the example given from the output of module spider we can drill down.

$ module spider bcftools/1.9_gcc-9.1.0

--------------------------------------------------------------------------------------------------------------------
  bcftools: bcftools/1.9_gcc-9.1.0
--------------------------------------------------------------------------------------------------------------------


    You will need to load all module(s) on any one of the lines below before the "bcftools/1.9_gcc-9.1.0" module is avai
lable to load.


      stack/2019.1

So we can load that version of bcftools by first loading stack/2019.1 module.

$ module load stack/2019.1
$ module load bcftools/1.9_gcc-9.1.0

Note that newer versions of packages will become the default after loading a "stack" module so be careful with versions. 

The module system can also automatically swap versions for you but be careful to check that it is loading the module versions that you want. This will only work if you have not specified an explicit version. For example,

$ module purge
$ module load bcftools
$ module list bcftools

Currently Loaded Modules Matching: bcftools
  1) bcftools/1.3.1


$ module load stack/2019.1

The following have been reloaded with a version change:
  1) bcftools/1.3.1 => bcftools/1.9_gcc-9.1.0     3) zlib/1.2.11 => zlib/1.2.11_gcc-9.1.0
  2) htslib/1.3.2 => htslib/1.9_gcc-9.1.0


$ module list bcftools


Currently Loaded Modules Matching: bcftools
  1) bcftools/1.9_gcc-9.1.0



None of the new module stacks are loaded by default, mostly because this changes defaults. In addition, the original set of modules is always loaded. The idea is that you lay newer versions of packages on top of the older versions. You can swap one stack for another. Continuing with the bcftools example.

$ module list bcftools


Currently Loaded Modules Matching: bcftools
  1) bcftools/1.9_gcc-9.1.0

$ module load stack/2020.1 


Inactive Modules:
  1) libzip/1.2.0_gcc-9.1.0


The following have been reloaded with a version change:
  1) bcftools/1.9_gcc-9.1.0 => bcftools/1.10.2_intel-19.0.5.281
  2) bzip2/1.0.6_gcc-9.1.0 => bzip2/1.0.8_intel-19.0.5.281
  3) curl/7.52.1 => curl/7.63.0_intel-19.0.5.281
  4) gsl/2.3 => gsl/2.5_intel-19.0.5.281
  5) htslib/1.9_gcc-9.1.0 => htslib/1.10.2_intel-19.0.5.281
  6) stack/2019.1 => stack/2020.1
  7) xz/5.2.4_gcc-9.1.0 => xz/5.2.4_intel-19.0.5.281
  8) zlib/1.2.11_gcc-9.1.0 => zlib/1.2.11_intel-19.0.5.281



$ module list bcftools                                                                           


Currently Loaded Modules Matching: bcftools
  1) bcftools/1.10.2_intel-19.0.5.281


The above also shows why you have to verify that the auto swapping is correct as you can see that now the compiler has changed, which may not be what you want.

Original software stack

The environment modules for these packages are always visible. There are packages here that are not yet in the newer stacks.

 Click here to expand...

ProgramVersionLink to main page
bamtools2.5.1pezmaster31/bamtools: C++ API & command-line toolkit for working with BAM data
augustus3.3.2Augustus: gene prediction
cmake

3.7.2
3.13.2

CMake - Cross Platform Make

RHash1.3.7rhash/RHash: Great utility for computing hash sums
FFTW3.3.6
3.3.7
FFTW Home Page
GCC

5.4.0
6.3.0
7.3.0
8.3.0

GCC, the GNU Compiler Collection - GNU Project - Free Software Foundation (FSF)
GMP6.1.2The GNU MP Bignum Library
grib_api1.19.0 Home - GRIB-API - ECMWF Confluence Wiki
GSL2.2.3GSL - GNU Scientific Library - GNU Project - Free Software Foundation (FSF)
Gurobi Optimizer

5.6.3
7.0.2
8.1.0
9.0.0

Gurobi Optimizer
HDF51.8.18HDF Group - HDF5
Intel Parallel Studio
  • Intel compilers
  • MKL
  • DAAL
  • IPP
  • TBB

2017.1
2017.4

Intel® Composer XE Suites
Intel-MKL2019.3.199Intel® Math Kernel Library (Intel® MKL) | Intel® Software
matlab

R2016b
2018a

MATLAB - The Language of Technical Computing
MPC1.0.3MPC
MPFR3.1.5

The GNU MPFR Library

NCO4.6.4NCO Homepage
netcdf4.4.1.1Unidata | NetCDF
netcdf-cxx4.3.0Unidata | NetCDF
netcdf-fortran4.4.4Unidata | NetCDF

openmpi

2.0.1
2.1.2
Open MPI: Open Source High Performance Computing
PythonWelcome to Python.org
RThe R Project for Statistical Computing
valgrind3.12.0Valgrind Home
ocaml4.04.0 OCaml
Ansys

17.2 

ANSYS - Simulation Driven Product Development
CFITSIO3.410FITSIO Home Page
Pythia8.223PYTHIA
Platypus0.8.1Platypus Variant Caller
Ruby

2.4.0

Ruby Programming Language
Julia0.5.0
0.5.1
The Julia Language
MOSEK8.0.0.53
8.0.0.80
MOSEK ApS
JDK8u121
8u172
Java SE | Oracle Technology Network | Oracle
RSL1.49RSL (Radar Software Library)
Perl5.24.1The Perl Programming Language
Postgresql11.2PostgreSQL: The world's most advanced open source database
Graphviz2.40.1

Graphviz - Graph Visualization Software

htslib1.3.2Releases · samtools/htslib
samtools1.3.1Releases · samtools/samtools
bcftools1.3.1Releases · samtools/bcftools
bedtools2.26.0bedtools: a powerful toolset for genome arithmetic
lzo2.09

LZO real-time data compression library

CUDA8.0.44
8.0.61
9.0.176.1
9.1.85.1
9.1.85.2
Parallel Programming and Computing Platform | CUDA | NVIDIA
Beagle-lib2.1.2
3.1.2
general purpose library for evaluating the likelihood of sequence evolution on trees
Tecplot3602016R2Tecplot 360 CFD post processing tools to analyze data
CDO1.8.0Overview - CDO
I/O API3.2CMAS: Community Modeling and Analysis System I/O API
Plink1.07PLINK: Whole genome data analysis toolset
CMAQ5.1Community Multi-scale Air Quality (CMAQ) Modeling System for Air Quality Management | Air Research | US EPA
NCL6.4.0NCL Overview
HDF-EOS22.19HDF-EOS Tools and Information Center
HDF-EOS51.15HDF-EOS Tools and Information Center
g2clib1.60

GRIB2

Gaussian 09D.01Gaussian.com | Expanding the limits of computational chemistry
NBO6.0NATURAL BOND ORBITAL 6.0 HOME
HDF4.2.1HDF Group - HDF4
AutoDock Vina1.1.2AutoDock Vina - molecular docking and virtual screening program
BEAST1.8.4BEAST Software - Bayesian Evolutionary Analysis Sampling Trees
XCrySDen1.5.60XCrySDen - (X-Window) Crystalline Structures and Densities
Mesa17.0.1The Mesa 3D Graphics Library
LLVM4.0.0The LLVM Compiler Infrastructure Project
Open Babel2.4.1Open Babel
Eigen3.3.3Eigen
Protobuf (C++)3.2.0Protocol Buffers  |  Google Developers
Snappy1.1.4Snappy by google
LevelDB1.20GitHub - google/leveldb: LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.
YASM1.3.0The Yasm Modular Assembler Project
FFMPEG3.2.4About FFmpeg
OpenCV3.2.0OpenCV library
JAGS4.2.0JAGS - Just Another Gibbs Sampler
STAR-CCM+

12.02.010 
13.04.010

STAR-CCM+® | CFD Simulation Software
Cufflinks2.2.1Cufflinks
PETSc
  • hpre
  • metis
  • parmetis
  • mpi4py
  • mumps
  • petsc4py
  • ptscotch
  • suitesparse
  • superlu_dist 
3.7.5
3.10.3
PETSc: Home Page
Wannier902.1.0wannier.org
Atompaw4.0.0.14Atompaw Web Page
Libxc2.2.3
3.0.0 
Libxc - OctopusWiki
ABINIT8.2.2ABINIT
c-blosc1.11.2Blosc, an extremely fast, multi-threaded, meta-compressor library | Blosc Main Page
MDTraj1.8.0MDTraj
lmfit6.1lmfit [MLZ Scientific Computing Group]
Gromacs2016.3Gromacs
ELPA2016.05.004
2018.11.001
About ELPA — Eigenvalue SoLvers for Petaflop-Applications (ELPA)
Quantum Espresso6.1Quantum ESPRESSO
BWA0.7.15Burrows-Wheeler Aligner
libcerf1.5libcerf [MLZ Scientific Computing Group]
Gnuplot5.0.6gnuplot homepage
GEOS3.6.1GEOS
Ncview2.1.7Ncview
git2.13.0Git
BLAST
databases: nt, nt, swissprot
2.6.0+BLAST: Basic Local Alignment Search Tool
ParaView5.4.0ParaView Home
cuDNN5.1
6.0
7.0.5
NVIDIA cuDNN | NVIDIA Developer
Leptonica1.74.4Leptonica
Tesseract3.05.01Tesseract Open Source OCR Engine
WebP0.6.0A new image format for the Web  |  WebP  |  Google Developers
giflib5.1.4The GIFLIB project
Subread1.5.2Subread
GLPK4.62

GLPK - GNU Project - Free Software Foundation (FSF)

Symphony5.6.16SYMPHONY
gavl1.4.0Gmerlin homepage - gavl
frei0r-plugins1.6.1Frei0r :: Free Video Effects collection
MPFI1.5.1InriaForge: MPFI: Project Home
ESBTL1.0-beta01ESBTL (Easy Structural Biology Template Library)
gf2x1.2InriaForge: gf2x: Project Home
NTL10.4.0NTL: A Library for doing Number Theory
CGAL4.10
4.13
The Computational Geometry Algorithms Library
SQLite3.16.2
3.30.0
SQLite Home Page
scotch6.0.4SCOTCH: Static Mapping, Graph, Mesh and Hypergraph Partitioning, and Parallel and Sequential Sparse Matrix Ordering Package
metis5.1.0METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering | Karypis Lab
parmetis4.0.3ParMETIS - Parallel Graph Partitioning and Fill-reducing Matrix Ordering | Karypis Lab
OpenFOAM4.1
5.0
OpenFOAM | Free CFD Software | The OpenFOAM Foundation
STAR2.5.3aSTAR | Spliced Transcripts Alignment to a Reference
libunwind1.2.1The libunwind project
glog0.3.5google/glog: C++ implementation of the Google logging module
gflags2.2.1How To Use Gflags (formerly Google Commandline Flags)
LMDB0.9.21LMDB/lmdb: Read-only mirror of official repo on openldap.org.
Caffe1.0Caffe | Deep Learning Framework
NCCL1.3.4
2.1.4
NVIDIA/nccl: Optimized primitives for collective multi-GPU communication

WIEN2K

license required

17.1WIEN 2k
Turbomole

7.2.0

7.2.1

Turbomole: Program Package for ab initio Electronic Structure Calculations
Parallel NetCDF1.8.1parallel-netcdf
Amber2017 (Amber16 + AmberTools17)The Amber Molecular Dynamics Package
TransPS1.1.0TransPS
cusplibrary0.4.0
0.5.1
CUSP: Main Page
Mesquite2.3.0Mesquite – The Trilinos Project
foam-extend4.0foam-extend download | SourceForge.net
HPL2.2HPL - A Portable Implementation of the High-Performance Linpack Benchmark for Distributed-Memory Computers
PortAudio19.6.0PortAudio - an Open-Source Cross-Platform Audio API
openSMILE2.3.0audEERING | Intelligent Audio Engineering – openSMILE
log4j2.10.0Log4j – Apache Log4j 2 - Apache Log4j 2
flex2.6.4GitHub - westes/flex: The Fast Lexical Analyzer - scanner generator for lexing in C and C++
WRF
WRF-chem
WPS (WRF Preprocessing System)
3.9.1.1Weather Research and Forecasting Model | MMM: Mesoscale & Microscale Meteorology Laboratory
Darshan3.5.1Darshan
RngStreams1.0.1

RngStreams - multiple independent streams of pseudo-random numbers

UNU.RAN1.8.1UNU.RAN - Universal Non-Uniform RANdom number generators
LZ41.8.1.2LZ4 - Extremely fast compression
GL2PS1.4.0GL2PS: an OpenGL to PostScript printing library
XRootD4.8.1Home Page | XRootD
Z34.6.0GitHub - Z3Prover/z3: The Z3 Theorem Prover
Davix0.6.7GitHub - cern-it-sdc-id/davix: High-performance file management over WebDAV / HTTP
xxHash0.6.4GitHub - Cyan4973/xxHash
Oracle instantclient

12.2.0.1.0

Oracle Instant Client - Free tools and libraries for connecting to Oracle Database
ROOT6.12.06ROOT a Data analysis Framework
Praat6.0.37Praat: doing Phonetics by Computer
MKL-DNN0.12GitHub - intel/mkl-dnn: Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN)
NASM2.13.03NASM
Yeppp1.0.0MDukhan / Yeppp — Bitbucket
CNVnator0.3.3GitHub - abyzovlab/CNVnator: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
CPLEX12.8.0ILOG CPLEX Optimization Studio | IBM
9.4_TS1M2Foundation Tools | SAS
Gentle0.10.1lowerquality/gentle: gentle forced aligner
Bazel0.12.0Bazel - a fast, scalable, multi-language and extensible build system - Bazel
TensorBoard1.7.0tensorflow/tensorboard: TensorFlow's Visualization Toolkit
TensorFlow1.7.0TensorFlow
libedit3.1-20170329Editline Library (libedit) - Port of NetBSD Command Line Editor Library
GEANT410.4.1Overview | geant4.web.cern.ch
Google Test1.8.0google/googletest: Google Test
InsightToolkit4.13.0
4.13.2
ITK - Segmentation & Registration Toolkit
RTK1.4.0RTK - Reconstruction Toolkit
Gate8.1Forewords | GATE
SimplElastix0.10.0SimpleElastix
Elastix4.9.0elastix
PGI Community Edition18.4PGI | Products | Community Edition
Nettle3.4Nettle - a low-level crypto library
libarchive3.3.2libarchive - C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats
SRA-tools2.9.0ncbi/sra-tools: SRA Tools
NGS2.9.0ncbi/ngs: NGS Language Bindings
NCBI-VDB2.9.0-1ncbi/ncbi-vdb: ncbi-vdb
LASzip2.2.0
3.2.2
LASzip - free and lossless LiDAR compression
libLAS1.8.1libLAS - LAS 1.0/1.1/1.2 ASPRS LiDAR data translation toolset — liblas.org
libgeotiff1.4.2GeoTIFF
libgpuarray0.7.6Welcome to libgpuarray’s documentation!
GATK4.0.5.2GATK | Home
SNAP0.15SNAP Sequence Aligner
zstd1.3.5

Zstandard - Real-time data compression algorithm

magma2.4.0Magma
ZeroMQ4.2.5Distributed Messaging
CUB1.8.0CUB: Main Page
pybind112.2.3pybind/pybind11: Seamless operability between C++11 and Python
pytorch/caffe20.4.0PyTorch
torchvision0.2.1pytorch/vision: Datasets, Transforms and Models specific to Computer Vision
bowtie1.2.2Bowtie: An ultrafast, memory-efficient short read aligner
bowtie22.3.4.2Bowtie 2: fast and sensitive read alignment
WRF-Hydro5.0.0Overview | NCAR Research Applications Laboratory | RAL
libuuid1.0.3libuuid download | SourceForge.net
CZMQ4.1.1CZMQ - High-level C Binding for ZeroMQ - libzapi
cppzmq4.3.0zeromq/cppzmq: Header-only C++ binding for libzmq
libtool2.4.6GNU Libtool - GNU Project - Free Software Foundation
libunistring0.9.10libunistring - GNU Project - Free Software Foundation (FSF)
libatomic_ops7.6.4ivmai/libatomic_ops: The atomic_ops project (Atomic memory update operations portable implementation)
GC7.6.4A garbage collector for C and C++
Guile2.2.4GNU's programming and extension language — GNU Guile
libctl4.1.3Overview - libctl Documentation
OpenBUGS3.2.3FrontPage - OpenBUGS
TopHat2.1.1
2.1.2
TopHat
VCFtools0.1.16VCFtools
Jellyfish2.2.10gmarcais/Jellyfish: A fast multi-threaded k-mer counter
BLAT35Human BLAT Search
Mapsembler22.2.4mapsembler2
cortex_con0.04c (beta)CORTEX website (cortex_con)
cortex_var1.0.5.21CORTEX website (cortex_var)
CoNIFER0.2.2Conifer - COpy Number Inference From Exome Reads - Home
libgtextutils0.7agordon/libgtextutils: Gordon's Text utils Library
fastx_toolkit0.0.14agordon/fastx_toolkit: FASTA/FASTQ pre-processing programs

Abaqus

license required

2018Abaqus Unified FEA - SIMULIA™ by Dassault Systèmes®
GMT5.4.4GenericMappingTools/gmt: The Generic Mapping Tools
RocksDB5.17.2RocksDB | A persistent key-value store | RocksDB
TeXLive20180414TeX Live - TeX Users Group
ARPACK-NG3.7.0opencollab/arpack-ng: Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
SuperLU5.2.1SuperLU: Home Page
Armadillo9.200.7Armadillo: C++ library for linear algebra & scientific computing
PEST13.6PESThomePage.org - HOME PAGE
FEniCS2018.1.0FEniCS Project
mpiP3.4.1mpiP: Lightweight, Scalable MPI Profiling
PAPI5.7.0PAPI
SimpleITK1.2.0SimpleITK
OpenJDK11.0.2OpenJDK
libogg1.3.3Xiph.org
flac1.3.2FLAC - Free Lossless Audio Codec
mpg1231.25.10mpg123, Fast MP3 Player for Linux and UNIX systems
libvorbis1.3.6Xiph.org
libsndfile1.0.28Libsndfile
lame3.100LAME MP3 Encoder
libmad0.15.1bUnderbit: MAD (MPEG Audio Decoder)
libid3tag0.15.1bUnderbit: MAD (MPEG Audio Decoder)
opus1.3.1Opus Codec
wavpack5.1.0WavPack Audio Compression
TwoLAME0.3.13TwoLAME - MPEG Audio Layer 2 Encoder
libao1.2.0Xiph.org: libao: a cross platform audio library
opencore-amr0.1.5opencore-amr download | SourceForge.net
opusfile0.11Opus Codec
SoX14.4.2http://sox.sourceforge.net/
SCons3.0.5SCons: A software construction tool - SCons
ISCE22.3.1

isce-framework/isce2: InSAR Scientific Computing Environment version 2

Mono5.18.0.240Home | Mono
VASP5.4.4VASP - Vienna Ab initio Simulation Package
zip3.0Info-ZIP Home Page


Additional Software Stacks

These software stacks are made available by loading the environment module that corresponds to the stack version. That will make the modules available to be loaded. For instance,

module load stack/2019.1

 2020.1 (click to expand)

Package
(links to external page)

Versions Description

matlab

R2019b
 Click here to expand...

MATLAB (MATrix LABoratory) is a multi-paradigm numerical computing environment and fourth-generation programming language. A proprietary programming language developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, C#, Java, Fortran and Python.

gcc

4.9.4
6.3.0
8.3.0
9.2.0

 Click here to expand...

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.

intel

19.0.5
 Click here to expand...

Intel Compilers.

alsa-lib

1.1.4.1_gcc-4.9.4
1.1.4.1_gcc-8.3.0
1.1.4.1_gcc-9.2.0

 Click here to expand...

The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. alsa-lib contains the user space library that developers compile ALSA applications against.

atk

2.30.0_gcc-8.3.0
2.30.0_gcc-9.2.0

 Click here to expand...

ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.

at-spi2-atk

2.26.2_gcc-8.3.0
2.26.2_gcc-9.2.0

 Click here to expand...

The At-Spi2 Atk package contains a library that bridges ATK to At-Spi2 D-Bus service.

at-spi2-core

2.28.0_gcc-8.3.0
2.28.0_gcc-9.2.0

 Click here to expand...

The At-Spi2 Core package provides a Service Provider Interface for the Assistive Technologies available on the GNOME platform and a library against which applications can be linked.

augustus

3.3.2_gcc-4.9.4
3.3.2_gcc-9.2.0

 Click here to expand...

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

awscli

1.16.308_gcc-4.9.4
1.16.308_gcc-8.3.0
1.16.308_gcc-9.2.0
1.16.308_intel-19.0.5.281

 Click here to expand...

This package provides a unified command line interface to Amazon Web Services

bamtools

2.5.1_gcc-4.9.4
2.5.1_gcc-9.2.0

 Click here to expand...

C++ API & command-line toolkit for working with BAM data.

bart

0.5.00_gcc-8.3.0
 Click here to expand...

BART: Toolbox for Computational Magnetic Resonance Imaging

bcftools

1.10.2_gcc-4.9.4
1.10.2_gcc-8.3.0
1.10.2_gcc-9.2.0
1.10.2_intel-19.0.5.281

 Click here to expand...

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

beast1

1.10.4_gcc-8.3.0
 Click here to expand...

BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.

bedtools2

2.27.1_gcc-4.9.4
2.27.1_gcc-8.3.0
2.27.1_gcc-9.2.0
2.27.1_intel-19.0.5.281

 Click here to expand...

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.

binutils

2.32_gcc-4.9.4
2.32_gcc-8.3.0
2.32_gcc-9.2.0

 Click here to expand...

GNU binutils, which contain the linker, assembler, objdump and others

blast-plus

2.9.0_gcc-4.9.4
 Click here to expand...

Basic Local Alignment Search Tool.

blat

35_gcc-9.2.0
 Click here to expand...

BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm.

boost

1.70.0_gcc-4.9.4
1.70.0_gcc-9.2.0

 Click here to expand...

Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library.

bowtie

1.2.3_gcc-9.2.0
 Click here to expand...

Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

bowtie2

2.3.5.1_gcc-9.2.0
 Click here to expand...

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

braker

2.1.4_gcc-9.2.0
 Click here to expand...

BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS

bzip2

1.0.8_gcc-4.9.4
1.0.8_gcc-8.3.0
1.0.8_gcc-9.2.0
1.0.8_intel-19.0.5.281

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bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

cairo

1.16.0_gcc-4.9.4
1.16.0_gcc-8.3.0
1.16.0_gcc-9.2.0
1.16.0_intel-19.0.5.281

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Cairo is a 2D graphics library with support for multiple output devices.

c-ares

1.15.0_gcc-8.3.0
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c-ares: A C library for asynchronous DNS requests

c-blosc

1.17.0_gcc-4.9.4
1.17.0_gcc-8.3.0
1.17.0_gcc-9.2.0
1.17.0_intel-19.0.5.281

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Blosc, an extremely fast, multi-threaded, meta-compressor library

check

0.12.0_gcc-8.3.0
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Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.

cmake

3.16.2_gcc-4.9.4
3.16.2_gcc-8.3.0
3.16.2_gcc-9.2.0
3.16.2_intel-19.0.5.281

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A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

cp2k

6.1_intel-19.0.5.281
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CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems

cuda

10.1.243_gcc-8.3.0
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CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).

cudnn

7.6.5.32-10.1-linux-x64_gcc-8.3.0
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NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks

curl

7.63.0_gcc-4.9.4
7.63.0_gcc-8.3.0
7.63.0_gcc-9.2.0
7.63.0_intel-19.0.5.281

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cURL is an open source command line tool and library for transferring data with URL syntax

dbus

1.12.8_gcc-8.3.0
1.12.8_gcc-9.2.0

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D-Bus is a message bus system, a simple way for applications to talk to one another. D-Bus supplies both a system daemon (for events such new hardware device printer queue ) and a per-user-login-session daemon (for general IPC needs among user applications). Also, the message bus is built on top of a general one-to-one message passing framework, which can be used by any two applications to communicate directly (without going through the message bus daemon).

diamond

0.9.25_gcc-9.2.0
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DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

double-conversion

2.0.1_gcc-4.9.4
2.0.1_gcc-8.3.0
2.0.1_gcc-9.2.0
2.0.1_intel-19.0.5.281

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This project (double-conversion) provides binary-decimal and decimal-binary routines for IEEE doubles.

eigen

3.3.7_gcc-8.3.0
3.3.7_gcc-9.2.0

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Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and related algorithms.

elpa

2019.05.002_intel-19.0.5.281
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Eigenvalue solvers for Petaflop-Applications (ELPA)

emacs

26.3_gcc-9.2.0
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The Emacs programmable text editor.

exonerate

2.4.0_gcc-4.9.4
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Pairwise sequence alignment of DNA and proteins

expat

2.2.9_gcc-4.9.4
2.2.9_gcc-8.3.0
2.2.9_gcc-9.2.0
2.2.9_intel-19.0.5.281

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Expat is an XML parser library written in C.

fastx-toolkit

0.0.14_gcc-9.2.0
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The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

ffmpeg

4.2.2_gcc-4.9.4
4.2.2_gcc-8.3.0
4.2.2_gcc-9.2.0

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FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.

fftw

3.3.8_gcc-4.9.4
3.3.8_gcc-8.3.0
3.3.8_gcc-9.2.0
3.3.8_intel-19.0.5.281

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FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

fixesproto

5.0_gcc-8.3.0
5.0_gcc-9.2.0

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X Fixes Extension.

flac

1.3.2_gcc-4.9.4
1.3.2_gcc-8.3.0
1.3.2_gcc-9.2.0

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Encoder/decoder for the Free Lossless Audio Codec

fontconfig

2.12.3_gcc-4.9.4
2.12.3_gcc-8.3.0
2.12.3_gcc-9.2.0
2.12.3_intel-19.0.5.281

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Fontconfig is a library for configuring/customizing font access

font-util

1.3.2_gcc-4.9.4
1.3.2_gcc-8.3.0
1.3.2_gcc-9.2.0
1.3.2_intel-19.0.5.281

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X.Org font package creation/installation utilities and fonts.

fox

1.6.57_gcc-9.2.0
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FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation. FOX also implements icons, images, and user-convenience features such as status line help, and tooltips. Tooltips may even be used for 3D objects!

freeglut

3.0.0_gcc-9.2.0
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FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library

freetype

2.10.1_gcc-4.9.4
2.10.1_gcc-8.3.0
2.10.1_gcc-9.2.0
2.7.1_intel-19.0.5.281

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FreeType is a freely available software library to render fonts. It is written in C, designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images) of most vector and bitmap font formats.

gdal

3.0.2_gcc-4.9.4
3.0.2_gcc-8.3.0
3.0.2_gcc-9.2.0
3.0.2_intel-19.0.5.281

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GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command line utilities for data translation and processing.

gdbm

1.18.1_gcc-4.9.4
1.18.1_gcc-8.3.0
1.18.1_gcc-9.2.0
1.18.1_intel-19.0.5.281

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GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database.

gdk-pixbuf

2.38.0_gcc-8.3.0
2.38.0_gcc-9.2.0

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The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

genemark-et

4.46_gcc-9.2.0
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Gene Prediction in Bacteria, archaea, Metagenomes and Metatranscriptomes. When downloaded this file is named the same for all versions. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

genrich

0.6_gcc-9.2.0
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Genrich is a peak-caller for genomic enrichment assays.

geos

3.7.2_gcc-4.9.4
3.7.2_gcc-8.3.0
3.7.2_gcc-9.2.0
3.7.2_intel-19.0.5.281

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GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.

gettext

0.20.1_gcc-4.9.4
0.20.1_gcc-8.3.0
0.20.1_gcc-9.2.0
0.20.1_intel-19.0.5.281

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GNU internationalization (i18n) and localization (l10n) library.

ghostscript

9.26_gcc-8.3.0
9.26_gcc-9.2.0

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An interpreter for the PostScript language and for PDF.

gl2ps

1.3.9_gcc-9.2.0
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GL2PS is a C library providing high quality vector output for any OpenGL application.

glew

2.0.0_gcc-8.3.0
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The OpenGL Extension Wrangler Library.

glib

2.56.3_gcc-4.9.4
2.56.3_gcc-8.3.0
2.56.3_gcc-9.2.0
2.56.3_intel-19.0.5.281

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GLib provides the core application building blocks for libraries and applications written in C.

glpk

4.65_gcc-4.9.4
4.65_gcc-8.3.0
4.65_gcc-9.2.0
4.65_intel-19.0.5.281

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The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.

gmp

6.1.2_gcc-4.9.4
6.1.2_gcc-8.3.0
6.1.2_gcc-9.2.0
6.1.2_intel-19.0.5.281

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GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.

gnuplot

5.2.7_gcc-8.3.0
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Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986

gnutls

3.6.8_gcc-4.9.4
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GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.

gobject-introspection

1.56.1_gcc-4.9.4
1.56.1_gcc-8.3.0
1.56.1_gcc-9.2.0
1.56.1_intel-19.0.5.281

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The GObject Introspection is used to describe the program APIs and collect them in a uniform, machine readable format.Cairo is a 2D graphics library with support for multiple output

gpu-burn

1.0_gcc-8.3.0
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Multi-GPU CUDA stress test. Note that the file pointed to by COMPARE_PTX needs to be copied or linked to the current working directory before running gpu_burn.

graphite2

1.3.13_gcc-4.9.4
1.3.13_gcc-8.3.0
1.3.13_gcc-9.2.0
1.3.13_intel-19.0.5.281

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Graphite is a system that can be used to create 'smart fonts' capable of displaying writing systems with various complex behaviors. A smart font contains not only letter shapes but also additional instructions indicating how to combine and position the letters in complex ways.

graphviz

2.42.2_gcc-4.9.4
2.42.2_gcc-8.3.0
2.42.2_gcc-9.2.0
2.42.2_intel-19.0.5.281

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Graph Visualization Software

gsl

2.5_gcc-4.9.4
2.5_gcc-8.3.0
2.5_gcc-9.2.0
2.5_intel-19.0.5.281

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The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

gtkplus

3.20.10_gcc-8.3.0
3.20.10_gcc-9.2.0

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The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

harfbuzz

2.1.3_intel-19.0.5.281
2.3.1_gcc-4.9.4
2.3.1_gcc-8.3.0
2.3.1_gcc-9.2.0

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The Harfbuzz package contains an OpenType text shaping engine.

hdf

4.2.14_gcc-4.9.4
4.2.14_gcc-8.3.0
4.2.14_gcc-9.2.0
4.2.14_intel-19.0.5.281

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HDF4 (also known as HDF) is a library and multi-object file format for storing and managing data between machines.

hdf5

1.10.5_gcc-4.9.4
1.10.5_gcc-8.3.0
1.10.5_gcc-9.2.0
1.10.5_intel-19.0.5.281

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HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

hmmer

3.2.1_gcc-4.9.4
3.3_gcc-9.2.0

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HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

hpl

2.3_intel-19.0.5.281
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HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.

htslib

1.10.2_gcc-4.9.4
1.10.2_gcc-8.3.0
1.10.2_gcc-9.2.0
1.10.2_intel-19.0.5.281

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C library for high-throughput sequencing data formats.

hwloc

1.11.11_gcc-4.9.4
1.11.11_gcc-8.3.0
1.11.11_gcc-9.2.0
1.11.11_intel-19.0.5.281

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The Hardware Locality (hwloc) software project.

hypre

2.18.2_gcc-9.2.0
2.18.2_intel-19.0.5.281

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Hypre is a library of high performance preconditioners that features parallel multigrid methods for both structured and unstructured grid problems.

icu4c

65.1_gcc-4.9.4
65.1_gcc-8.3.0
65.1_gcc-9.2.0
65.1_intel-19.0.5.281

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ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU4C is the C/C++ interface.

id3lib

3.8.3_gcc-4.9.4
3.8.3_gcc-8.3.0
3.8.3_gcc-9.2.0

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Library for manipulating ID3v1 and ID3v2 tags

inputproto

2.3.2_gcc-8.3.0
2.3.2_gcc-9.2.0

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X Input Extension.

intel-mkl

2019.5.281_gcc-4.9.4
2019.5.281_gcc-8.3.0
2019.5.281_gcc-9.2.0
2019.5.281_intel-19.0.5.281

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Intel Math Kernel Library.

intel-tbb

2019.8_gcc-9.2.0
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Widely used C++ template library for task parallelism. Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.

intel-xed

2019.03.01_gcc-9.2.0
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The Intel X86 Encoder Decoder library for encoding and decoding x86 machine instructions (64- and 32-bit). Also includes libxed-ild, a lightweight library for decoding the length of an instruction.

interproscan

4.8_gcc-4.9.4
5.38-76.0_gcc-9.2.0

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InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.

jags

4.3.0_gcc-4.9.4
4.3.0_gcc-8.3.0
4.3.0_gcc-9.2.0
4.3.0_intel-19.0.5.281

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JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS

jasper

2.0.14_gcc-8.3.0
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Library for manipulating JPEG-2000 images

json-c

0.13.1_gcc-4.9.4
0.13.1_gcc-8.3.0
0.13.1_gcc-9.2.0
0.13.1_intel-19.0.5.281

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A JSON implementation in C.

jsoncpp

1.9.1_gcc-8.3.0
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JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.

julia

1.3.1_gcc-9.2.0
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The Julia Language: A fresh approach to technical computing

kbproto

1.0.7_gcc-4.9.4
1.0.7_gcc-8.3.0
1.0.7_gcc-9.2.0
1.0.7_intel-19.0.5.281

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X Keyboard Extension.

lcms

2.9_gcc-4.9.4
2.9_gcc-8.3.0
2.9_gcc-9.2.0
2.9_intel-19.0.5.281

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Little cms is a color management library. Implements fast transforms between ICC profiles. It is focused on speed, and is portable across several platforms (MIT license).

leveldb

1.22_gcc-8.3.0
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LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.

libbeagle

3.1.2_gcc-8.3.0
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Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

libbsd

0.10.0_gcc-4.9.4
0.10.0_gcc-8.3.0
0.10.0_gcc-9.2.0
0.10.0_intel-19.0.5.281

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This library provides useful functions commonly found on BSD systems, and lacking on others like GNU systems, thus making it easier to port projects with strong BSD origins, without needing to embed the same code over and over again on each project.

libcerf

1.3_gcc-8.3.0
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A self-contained C library providing complex error functions, based on Faddeeva's plasma dispersion function w(z). Also provides Dawson's integral and Voigt's convolution of a Gaussian and a Lorentzian

libdrm

2.4.81_gcc-9.2.0
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A userspace library for accessing the DRM, direct rendering manager, on Linux, BSD and other systems supporting the ioctl interface.

libedit

3.1-20170329_gcc-4.9.4
3.1-20170329_gcc-8.3.0
3.1-20170329_gcc-9.2.0

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An autotools compatible port of the NetBSD editline library

libepoxy

1.4.3_gcc-8.3.0
1.4.3_gcc-9.2.0

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Epoxy is a library for handling OpenGL function pointer management for you.

libffi

3.2.1_gcc-4.9.4
3.2.1_gcc-8.3.0
3.2.1_gcc-9.2.0
3.2.1_intel-19.0.5.281

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The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time.

libgd

2.2.4_gcc-8.3.0
2.2.4_gcc-9.2.0

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GD is an open source code library for the dynamic creation of images by programmers. GD is written in C, and 'wrappers' are available for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, WebP, XPM, BMP images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development.

libgeotiff

1.5.1_gcc-4.9.4
1.5.1_gcc-8.3.0
1.5.1_gcc-9.2.0
1.5.1_intel-19.0.5.281

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GeoTIFF represents an effort by over 160 different remote sensing, GIS, cartographic, and surveying related companies and organizations to establish a TIFF based interchange format for georeferenced raster imagery.

libgit2

0.26.0_gcc-4.9.4
0.26.0_gcc-8.3.0
0.26.0_gcc-9.2.0
0.26.0_intel-19.0.5.281

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libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.

libgpuarray

0.7.5_gcc-8.3.0
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Make a common GPU ndarray(n dimensions array) that can be reused by all projects that is as future proof as possible, while keeping it easy to use for simple need/quick test.

libgtextutils

0.7_gcc-9.2.0
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Gordon's Text utils Library.

libice

1.0.9_gcc-4.9.4
1.0.9_gcc-8.3.0
1.0.9_gcc-9.2.0
1.0.9_intel-19.0.5.281

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libICE - Inter-Client Exchange Library.

libiconv

1.16_gcc-4.9.4
1.16_gcc-8.3.0
1.16_gcc-9.2.0
1.16_intel-19.0.5.281

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GNU libiconv provides an implementation of the iconv() function and the iconv program for character set conversion.

libjpeg-turbo

2.0.3_gcc-4.9.4
2.0.3_gcc-8.3.0
2.0.3_gcc-9.2.0
2.0.3_intel-19.0.5.281

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libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.

libmng

2.0.3_gcc-4.9.4
2.0.3_gcc-8.3.0
2.0.3_gcc-9.2.0
2.0.3_intel-19.0.5.281

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libmng -THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image-format.

libogg

1.3.2_gcc-4.9.4
1.3.2_gcc-8.3.0
1.3.2_gcc-9.2.0

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Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.

libpaper

1.1.28_gcc-8.3.0
1.1.28_gcc-9.2.0

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The paper library and accompanying files are intended to provide a simple way for applications to take actions based on a system- or user-specified paper size.

libpciaccess

0.13.5_gcc-4.9.4
0.13.5_gcc-8.3.0
0.13.5_gcc-9.2.0
0.13.5_intel-19.0.5.281

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Generic PCI access library.

libpng

1.6.37_gcc-4.9.4
1.6.37_gcc-8.3.0
1.6.37_gcc-9.2.0
1.6.37_intel-19.0.5.281

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libpng is the official PNG reference library.

libpthread-stubs

0.4_gcc-4.9.4
0.4_gcc-8.3.0
0.4_gcc-9.2.0
0.4_intel-19.0.5.281

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The libpthread-stubs package provides weak aliases for pthread functions not provided in libc or otherwise available by default.

libsm

1.2.2_gcc-4.9.4
1.2.2_gcc-8.3.0
1.2.2_gcc-9.2.0
1.2.2_intel-19.0.5.281

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libSM - X Session Management Library.

libsndfile

1.0.28_gcc-4.9.4
1.0.28_gcc-8.3.0
1.0.28_gcc-9.2.0

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Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. It is released in source code format under the Gnu Lesser General Public License.

libsodium

1.0.17_gcc-4.9.4
1.0.17_gcc-8.3.0
1.0.17_gcc-9.2.0
1.0.17_intel-19.0.5.281

 Click here to expand...

Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.

libssh2

1.8.0_gcc-4.9.4
1.8.0_gcc-8.3.0
1.8.0_gcc-9.2.0
1.8.0_intel-19.0.5.281

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libssh2 is a client-side C library implementing the SSH2 protocol

libtiff

4.0.10_gcc-4.9.4
4.0.10_gcc-8.3.0
4.0.10_gcc-9.2.0
4.0.10_intel-19.0.5.281

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LibTIFF - Tag Image File Format (TIFF) Library and Utilities.

libtool

2.4.6_gcc-4.9.4
2.4.6_gcc-8.3.0
2.4.6_gcc-9.2.0
2.4.6_intel-19.0.5.281

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libtool – library building part of autotools.

libvorbis

1.3.5_gcc-4.9.4
1.3.5_gcc-8.3.0
1.3.5_gcc-9.2.0

 Click here to expand...

Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format for mid to high quality (8kHz- 48.0kHz, 16+ bit, polyphonic) audio and music at fixed and variable bitrates from 16 to 128 kbps/channel.

libx11

1.6.7_gcc-4.9.4
1.6.7_gcc-8.3.0
1.6.7_gcc-9.2.0
1.6.7_intel-19.0.5.281

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libX11 - Core X11 protocol client library.

libxau

1.0.8_gcc-4.9.4
1.0.8_gcc-8.3.0
1.0.8_gcc-9.2.0
1.0.8_intel-19.0.5.281

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The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.

libxaw

1.0.13_gcc-8.3.0
1.0.13_gcc-9.2.0

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Xaw is the X Athena Widget Set. Xaw is a widget set based on the X Toolkit Intrinsics (Xt) Library.

libxcb

1.13_gcc-4.9.4
1.13_gcc-8.3.0
1.13_gcc-9.2.0
1.13_intel-19.0.5.281

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The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.

libxcursor

1.1.14_gcc-9.2.0
 Click here to expand...

libXcursor - X Window System Cursor management library.

libxdamage

1.1.4_gcc-9.2.0
 Click here to expand...

This package contains the library for the X Damage extension.

libxdmcp

1.1.2_gcc-4.9.4
1.1.2_gcc-8.3.0
1.1.2_gcc-9.2.0
1.1.2_intel-19.0.5.281

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libXdmcp - X Display Manager Control Protocol library.

libxext

1.3.3_gcc-4.9.4
1.3.3_gcc-8.3.0
1.3.3_gcc-9.2.0
1.3.3_intel-19.0.5.281

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libXext - library for common extensions to the X11 protocol.

libxfixes

5.0.2_gcc-8.3.0
5.0.2_gcc-9.2.0

 Click here to expand...

This package contains header files and documentation for the XFIXES extension. Library and server implementations are separate.

libxft

2.3.2_gcc-4.9.4
2.3.2_gcc-8.3.0
2.3.2_gcc-9.2.0
2.3.2_intel-19.0.5.281

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X FreeType library.

libxi

1.7.6_gcc-8.3.0
1.7.6_gcc-9.2.0

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libXi - library for the X Input Extension.

libxinerama

1.1.3_gcc-9.2.0
 Click here to expand...

libXinerama - API for Xinerama extension to X11 Protocol.

libxkbcommon

0.8.2_gcc-4.9.4
0.8.2_gcc-8.3.0
0.8.2_gcc-9.2.0
0.8.2_intel-19.0.5.281

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xkbcommon is a library to handle keyboard descriptions, including loading them from disk, parsing them and handling their state. It's mainly meant for client toolkits, window systems, and other system applications.

libxml2

2.9.9_gcc-4.9.4
2.9.9_gcc-8.3.0
2.9.9_gcc-9.2.0
2.9.9_intel-19.0.5.281

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Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License.

libxmu

1.1.2_gcc-4.9.4
1.1.2_gcc-8.3.0
1.1.2_gcc-9.2.0
1.1.2_intel-19.0.5.281

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This library contains miscellaneous utilities and is not part of the Xlib standard. It contains routines which only use public interfaces so that it may be layered on top of any proprietary implementation of Xlib or Xt.

libxpm

3.5.12_gcc-8.3.0
3.5.12_gcc-9.2.0

 Click here to expand...

libXpm - X Pixmap (XPM) image file format library.

libxrandr

1.5.0_gcc-9.2.0
 Click here to expand...

libXrandr - X Resize, Rotate and Reflection extension library.

libxrender

0.9.10_gcc-4.9.4
0.9.10_gcc-8.3.0
0.9.10_gcc-9.2.0
0.9.10_intel-19.0.5.281

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libXrender - library for the Render Extension to the X11 protocol.

libxscrnsaver

1.2.2_gcc-4.9.4
1.2.2_gcc-8.3.0
1.2.2_gcc-9.2.0
1.2.2_intel-19.0.5.281

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XScreenSaver - X11 Screen Saver extension client library

libxsmm

1.14_intel-19.0.5.281
 Click here to expand...

Library targeting Intel Architecture for specialized dense and sparse matrix operations, and deep learning primitives.

libxt

1.1.5_gcc-4.9.4
1.1.5_gcc-8.3.0
1.1.5_gcc-9.2.0
1.1.5_intel-19.0.5.281

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libXt - X Toolkit Intrinsics library.

libxxf86vm

1.1.4_gcc-9.2.0
 Click here to expand...

libXxf86vm - Extension library for the XFree86-VidMode X extension.

libyaml

0.2.2_gcc-4.9.4
0.2.2_gcc-8.3.0
0.2.2_gcc-9.2.0
0.2.2_intel-19.0.5.281

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A C library for parsing and emitting YAML.

libzmq

4.3.2_gcc-4.9.4
4.3.2_gcc-8.3.0
4.3.2_gcc-9.2.0
4.3.2_intel-19.0.5.281

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The ZMQ networking/concurrency library and core API

llvm

7.1.0_gcc-4.9.4
8.0.0_gcc-8.3.0
8.0.0_gcc-9.2.0
9.0.1_gcc-8.3.0
9.0.1_gcc-9.2.0

 Click here to expand...

The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines, though it does provide helpful libraries that can be used to build them. The name 'LLVM' itself is not an acronym; it is the full name of the project.

lmdb

0.9.24_gcc-4.9.4
0.9.24_gcc-8.3.0

 Click here to expand...

Symas LMDB is an extraordinarily fast, memory-efficient database we developed for the Symas OpenLDAP Project. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.

lz4

1.9.2_gcc-4.9.4
1.9.2_gcc-8.3.0
1.9.2_gcc-9.2.0
1.9.2_intel-19.0.5.281

 Click here to expand...

LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core, scalable with multi-cores CPU. It also features an extremely fast decoder, with speed in multiple GB/s per core, typically reaching RAM speed limits on multi-core systems.

lzo

2.10_gcc-4.9.4
2.10_gcc-8.3.0
2.10_gcc-9.2.0
2.10_intel-19.0.5.281

 Click here to expand...

Real-time data compression library

magma

2.5.1_gcc-8.3.0
 Click here to expand...

The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current 'Multicore+GPU' systems.

maker

2.31.10_gcc-4.9.4
 Click here to expand...

MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.

mariadb-c-client

3.1.4_gcc-4.9.4
3.1.4_gcc-8.3.0
3.1.4_gcc-9.2.0
3.1.4_intel-19.0.5.281

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MariaDB turns data into structured information in a wide array of applications, ranging from banking to websites. It is an enhanced, drop-in replacement for MySQL. MariaDB is used because it is fast, scalable and robust, with a rich ecosystem of storage engines, plugins and many other tools make it very versatile for a wide variety of use cases. This package comprises only the standalone 'C Connector', which enables connections to MariaDB and MySQL servers.

mesa-glu

9.0.0_gcc-8.3.0
9.0.0_gcc-9.2.0

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This package provides the Mesa OpenGL Utility library.

meson

0.49.1_gcc-8.3.0
0.49.1_gcc-9.2.0

 Click here to expand...

Meson is a portable open source build system meant to be both extremely fast, and as user friendly as possible.

metis

5.1.0_gcc-9.2.0
5.1.0_intel-19.0.5.281

 Click here to expand...

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.

mono

5.18.0.240_gcc-9.2.0
 Click here to expand...

Mono is a software platform designed to allow developers to easily create cross platform applications. It is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.

mpfr

4.0.2_gcc-4.9.4
4.0.2_gcc-8.3.0
4.0.2_gcc-9.2.0
4.0.2_intel-19.0.5.281

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The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

mumax

3.10beta_gcc-8.3.0
 Click here to expand...

GPU accelerated micromagnetic simulator.

mumps

5.2.0_gcc-9.2.0
5.2.0_intel-19.0.5.281

 Click here to expand...

MUMPS: a MUltifrontal Massively Parallel sparse direct Solver

ncbi-rmblastn

2.9.0_gcc-4.9.4
 Click here to expand...

RMBlast search engine for NCBI

nccl

2.4.8-1_gcc-8.3.0
 Click here to expand...

Optimized primitives for collective multi-GPU communication.

ncurses

6.1_gcc-4.9.4
6.1_gcc-8.3.0
6.1_gcc-9.2.0
6.1_intel-19.0.5.281

 Click here to expand...

The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD curses.

netcdf-c

4.7.3_gcc-4.9.4
4.7.3_gcc-8.3.0
4.7.3_gcc-9.2.0
4.7.3_intel-19.0.5.281

 Click here to expand...

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the C distribution.

netcdf-cxx

4.2_gcc-8.3.0
 Click here to expand...

Deprecated C++ compatibility bindings for NetCDF. These do NOT read or write NetCDF-4 files, and are no longer maintained by Unidata. Developers should migrate to current NetCDF C++ bindings, in Spack package netcdf-cxx4.

netcdf-cxx4

4.3.1_gcc-4.9.4
4.3.1_gcc-8.3.0
4.3.1_gcc-9.2.0
4.3.1_intel-19.0.5.281

 Click here to expand...

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the C++ distribution.

netcdf-fortran

4.5.2_gcc-4.9.4
4.5.2_gcc-8.3.0
4.5.2_gcc-9.2.0
4.5.2_intel-19.0.5.281

 Click here to expand...

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the Fortran distribution.

netlib-scalapack

2.1.0_gcc-9.2.0
2.1.0_intel-19.0.5.281

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ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines

nettle

3.4.1_gcc-4.9.4
 Click here to expand...

The Nettle package contains the low-level cryptographic library that is designed to fit easily in many contexts.

ngmerge

0.3_gcc-9.2.0
 Click here to expand...

Merging paired-end reads and removing adapters.

ninja

1.9.0_gcc-8.3.0
1.9.0_gcc-9.2.0

 Click here to expand...

Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible.

nlopt

2.5.0_gcc-4.9.4
2.5.0_gcc-8.3.0
2.5.0_gcc-9.2.0
2.5.0_intel-19.0.5.281

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NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.

numactl

2.0.12_gcc-4.9.4
2.0.12_gcc-8.3.0
2.0.12_gcc-9.2.0
2.0.12_intel-19.0.5.281

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NUMA support for Linux

openblas

0.3.10_gcc-9.2.0
0.3.10_intel-19.0.5.281

 Click here to expand...

OpenBLAS: An optimized BLAS library

opencv

4.1.0_gcc-8.3.0
 Click here to expand...

OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C+, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C+, the library can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware acceleration of the underlying heterogeneous compute platform. Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 9 million. Usage ranges from interactive art, to mines inspection, stitching maps on the web or through advanced robotics.

openjdk

11.0.2_gcc-4.9.4
11.0.2_gcc-8.3.0
11.0.2_gcc-9.2.0
11.0.2_intel-19.0.5.281

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The free and opensource java implementation

openmpi

3.1.5_gcc-4.9.4
3.1.5_gcc-8.3.0
3.1.5_gcc-9.2.0
3.1.5_intel-19.0.5.281

 Click here to expand...

An open source Message Passing Interface implementation.

openscenegraph

3.6.5_gcc-9.2.0
 Click here to expand...

OpenSceneGraph is an open source, high performance 3D graphics toolkit that's used in a variety of visual simulation applications.

openssl

1.1.1d_gcc-4.9.4
1.1.1d_gcc-8.3.0
1.1.1d_gcc-9.2.0
1.1.1d_intel-19.0.5.281

 Click here to expand...

OpenSSL is an open source project that provides a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library.

opus

1.1.4_gcc-9.2.0
 Click here to expand...

Opus is a totally open, royalty-free, highly versatile audio codec.

pandoc

2.7.3_gcc-8.3.0
2.7.3_gcc-9.2.0

 Click here to expand...

If you need to convert files from one markup format into another, pandoc is your swiss-army knife.

pango

1.41.0_gcc-4.9.4
1.41.0_gcc-8.3.0
1.41.0_gcc-9.2.0
1.41.0_intel-19.0.5.281

 Click here to expand...

Pango is a library for laying out and rendering of text, with an emphasis on internationalization. It can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit.

parallel-netcdf

1.12.1_gcc-4.9.4
1.12.1_gcc-8.3.0
1.12.1_gcc-9.2.0
1.12.1_intel-19.0.5.281

 Click here to expand...

PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5.

parmetis

4.0.3_gcc-9.2.0
4.0.3_intel-19.0.5.281

 Click here to expand...

ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.

pcre

8.42_gcc-4.9.4
8.42_gcc-8.3.0
8.42_gcc-9.2.0
8.42_intel-19.0.5.281

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The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.

pcre2

10.31_gcc-4.9.4
10.31_gcc-8.3.0
10.31_gcc-9.2.0
10.31_intel-19.0.5.281

 Click here to expand...

The PCRE2 package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.

perl

5.30.0_gcc-4.9.4
5.30.0_gcc-8.3.0
5.30.0_gcc-9.2.0
5.30.0_intel-19.0.5.281

 Click here to expand...

Perl 5 is a highly capable, feature-rich programming language with over 27 years of development.

perl-acme-damn

0.08_gcc-4.9.4
 Click here to expand...

Acme::Damn provides a single routine, damn(), which takes a blessed reference (a Perl object), and unblesses it, to return the original reference.

perl-algorithm-diff

1.1903_gcc-4.9.4
 Click here to expand...

Compute 'intelligent' differences between two files / lists

perl-bioperl

1.7.6_gcc-4.9.4
 Click here to expand...

BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are advertised to do in the documentation, but they also interact - Alignment objects are made from the Sequence objects, Sequence objects have access to Annotation and SeqFeature objects and databases, Blast objects can be converted to Alignment objects, and so on. This means that the objects provide a coordinated and extensible framework to do computational biology.

perl-bit-vector

7.4_gcc-4.9.4
 Click here to expand...

Efficient bit vector, set of integers and 'big int' math library

perl-capture-tiny

0.46_gcc-4.9.4
 Click here to expand...

Capture STDOUT and STDERR from Perl, XS or external programs

perl-carp-clan

6.06_gcc-4.9.4
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Report errors from perspective of caller of a 'clan' of modules

perl-cgi

4.40_gcc-4.9.4
 Click here to expand...

CGI - Handle Common Gateway Interface requests and responses

perl-class-data-inheritable

0.08_gcc-4.9.4
0.08_gcc-9.2.0

 Click here to expand...

For creating accessor/mutators to class data.

perl-clone-choose

0.010_gcc-9.2.0
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Checks several different modules which provides a clone() function and selects an appropriate one.

perl-data-stag

0.14_gcc-4.9.4
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Structured Tags datastructures

perl-dbd-pg

3.10.0_gcc-4.9.4
 Click here to expand...

DBD::Pg is a Perl module that works with the DBI module to provide access to PostgreSQL databases.

perl-dbd-sqlite

1.59_01_gcc-4.9.4
 Click here to expand...

DBD::SQLite - Self-contained RDBMS in a DBI Driver

perl-dbi

1.636_gcc-4.9.4
 Click here to expand...

The DBI is the standard database interface module for Perl. It defines a set of methods, variables and conventions that provide a consistent database interface independent of the actual database being used.

perl-devel-stacktrace

2.02_gcc-4.9.4
2.02_gcc-9.2.0

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An object representing a stack trace.

perl-devel-symdump

2.0604_gcc-4.9.4
 Click here to expand...

Devel::Symdump - dump symbol names or the symbol table

perl-encode-locale

1.05_gcc-4.9.4
 Click here to expand...

Determine the locale encoding

perl-error

0.17028_gcc-4.9.4
 Click here to expand...

The Error package provides two interfaces. Firstly Error provides a procedural interface to exception handling. Secondly Error is a base class for errors/exceptions that can either be thrown, for subsequent catch, or can simply be recorded.

perl-exception-class

1.43_gcc-4.9.4
1.43_gcc-9.2.0

 Click here to expand...

A module that allows you to declare real exception classes in Perl

perl-exporter-tiny

1.000000_gcc-4.9.4
 Click here to expand...

An exporter with the features of Sub::Exporter but only core dependencies

perl-file-copy-recursive

0.40_gcc-4.9.4
 Click here to expand...

Perl extension for recursively copying files and directories

perl-file-homedir

1.004_gcc-9.2.0
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Find your home and other directories on any platform

perl-file-listing

6.04_gcc-4.9.4
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Parse directory listing

perl-file-sharedir-install

0.11_gcc-4.9.4
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Install shared files

perl-file-which

1.22_gcc-4.9.4
1.22_gcc-9.2.0

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Perl implementation of the which utility as an API

perl-forks

0.36_gcc-4.9.4
 Click here to expand...

The 'forks' pragma allows a developer to use threads without having to have a threaded perl, or to even run 5.8.0 or higher.

perl-graph

0.9704_gcc-4.9.4
 Click here to expand...

Graph data structures and algorithms

perl-hash-merge

0.300_gcc-9.2.0
 Click here to expand...

Hash::Merge merges two arbitrarily deep hashes into a single hash.

perl-html-parser

3.72_gcc-4.9.4
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HTML parser class

perl-html-tagset

3.20_gcc-4.9.4
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Data tables useful in parsing HTML

perl-http-cookies

6.04_gcc-4.9.4
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HTTP cookie jars

perl-http-daemon

6.01_gcc-4.9.4
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A simple http server class

perl-http-date

6.02_gcc-4.9.4
 Click here to expand...

Date conversion routines

perl-http-message

6.13_gcc-4.9.4
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HTTP style message (base class)

perl-http-negotiate

6.01_gcc-4.9.4
 Click here to expand...

Choose a variant to serve

perl-inline

0.80_gcc-4.9.4
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Write Perl Subroutines in Other Programming Languages

perl-inline-c

0.78_gcc-4.9.4
 Click here to expand...

C Language Support for Inline

perl-io-all

0.87_gcc-4.9.4
 Click here to expand...

IO::All combines all of the best Perl IO modules into a single nifty object oriented interface to greatly simplify your everyday Perl IO idioms. It exports a single function called io, which returns a new IO::All object. And that object can do it all!

perl-io-html

1.001_gcc-4.9.4
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Open an HTML file with automatic charset detection.

perl-io-prompt

0.997004_gcc-4.9.4
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By default, this module exports a single function prompt. It prompts the user to enter some input, and returns an object that represents the user input.

perl-io-string

1.08_gcc-4.9.4
 Click here to expand...

Emulate file interface for in-core strings

perl-io-stringy

2.111_gcc-4.9.4
 Click here to expand...

This toolkit primarily provides modules for performing both traditional and object-oriented i/o) on things other than normal filehandles; in particular, IO::Scalar, IO::ScalarArray, and IO::Lines.

perl-io-tty

1.13_01_gcc-4.9.4
 Click here to expand...

IO::Tty is used internally by IO::Pty to create a pseudo-tty. You wouldn't want to use it directly except to import constants, use IO::Pty. For a list of importable constants, see IO::Tty::Constant.

perl-ipc-run

20180523.0_gcc-4.9.4
 Click here to expand...

IPC::Run allows you to run and interact with child processes using files, pipes, and pseudo-ttys. Both system()-style and scripted usages are supported and may be mixed. Likewise, functional and OO API styles are both supported and may be mixed.

perl-libwww-perl

6.33_gcc-4.9.4
 Click here to expand...

The libwww-perl collection is a set of Perl modules which provides a simple and consistent application programming interface to the World-Wide Web. The main focus of the library is to provide classes and functions that allow you to write WWW clients.

perl-libxml-perl

0.08_gcc-4.9.4
 Click here to expand...

libxml-perl is a collection of smaller Perl modules, scripts, and documents for working with XML in Perl. libxml-perl software works in combination with XML::Parser, PerlSAX, XML::DOM, XML::Grove and others.

perl-list-moreutils

0.428_gcc-4.9.4
 Click here to expand...

Provide the stuff missing in List::Util

perl-list-moreutils-xs

0.428_gcc-4.9.4
 Click here to expand...

List::MoreUtils::XS is a backend for List::MoreUtils. Even if it's possible (because of user wishes) to have it practically independent from List::MoreUtils, it technically depend on List::MoreUtils. Since it's only a backend, the API is not public and can change without any warning.

perl-logger-simple

2.0_gcc-9.2.0
 Click here to expand...

Implementation of the Simran-Log-Log and Simran-Error-Error modules

perl-lwp-mediatypes

6.02_gcc-4.9.4
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Guess media type for a file or a URL

perl-mailtools

2.21_gcc-4.9.4
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Perl module for handling mail

perl-module-build

0.4224_gcc-4.9.4
 Click here to expand...

Module::Build is a system for building, testing, and installing Perl modules. It is meant to be an alternative to ExtUtils::MakeMaker. Developers may alter the behavior of the module through subclassing in a much more straightforward way than with MakeMaker. It also does not require a make on your system - most of the Module::Build code is pure-perl and written in a very cross-platform way.

perl-net-http

6.17_gcc-4.9.4
 Click here to expand...

Low-level HTTP connection (client)

perl-object-insideout

4.05_gcc-9.2.0
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Implements inside-out objects as anonymous scalar references that are blessed into a class with the scalar containing the ID for the object (usually a sequence number).

perl-parallel-forkmanager

1.19_gcc-9.2.0
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A simple parallel processing fork manager

perl-parse-recdescent

1.967015_gcc-4.9.4
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Generate Recursive-Descent Parsers

perl-pegex

0.64_gcc-4.9.4
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Acmeist PEG Parser Framework

perl-perl-unsafe-signals

0.03_gcc-4.9.4
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Quoting perl581delta:

perl-scalar-list-utils

1.50_gcc-9.2.0
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Scalar::Util - A selection of general-utility scalar subroutines

perl-scalar-util-numeric

0.40_gcc-9.2.0
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This module exports a number of wrappers around perl's builtin grok_number function, which returns the numeric type of its argument, or 0 if it isn't numeric.

perl-set-scalar

1.29_gcc-4.9.4
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Set::Scalar - basic set operations

perl-sub-uplevel

0.2800_gcc-4.9.4
 Click here to expand...

apparently run a function in a higher stack frame

perl-sys-sigaction

0.23_gcc-4.9.4
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Prior to version 5.8.0 perl implemented 'unsafe' signal handling. The reason it is consider unsafe, is that there is a risk that a signal will arrive, and be handled while perl is changing internal data structures. This can result in all kinds of subtle and not so subtle problems. For this reason it has always been recommended that one do as little as possible in a signal handler, and only variables that already exist be manipulated.

perl-termreadkey

2.38_gcc-4.9.4
 Click here to expand...

Term::ReadKey is a compiled perl module dedicated to providing simple control over terminal driver modes (cbreak, raw, cooked, etc.,) support for non-blocking reads, if the architecture allows, and some generalized handy functions for working with terminals. One of the main goals is to have the functions as portable as possible, so you can just plug in 'use Term::ReadKey' on any architecture and have a good likelihood of it working.

perl-test-deep

1.127_gcc-4.9.4
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Extremely flexible deep comparison

perl-test-differences

0.64_gcc-4.9.4
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Test strings and data structures and show differences if not ok

perl-test-exception

0.43_gcc-4.9.4
 Click here to expand...

Test exception-based code

perl-test-most

0.35_gcc-4.9.4
 Click here to expand...

Most commonly needed test functions and features.

perl-test-requiresinternet

0.05_gcc-4.9.4
 Click here to expand...

Easily test network connectivity

perl-test-warn

0.30_gcc-4.9.4
 Click here to expand...

Perl extension to test methods for warnings

perl-text-diff

1.45_gcc-4.9.4
 Click here to expand...

Provides a basic set of services akin to the GNU diff utility.

perl-text-soundex

3.05_gcc-4.9.4
 Click here to expand...

Soundex is a phonetic algorithm for indexing names by sound, as pronounced in English. The goal is for names with the same pronunciation to be encoded to the same representation so that they can be matched despite minor differences in spelling

perl-timedate

2.30_gcc-4.9.4
 Click here to expand...

The parser contained here will only parse absolute dates, if you want a date parser that can parse relative dates then take a look at the Time modules by David Muir on CPAN.

perl-try-tiny

0.28_gcc-4.9.4
 Click here to expand...

Minimal try/catch with proper preservation of $@

perl-uri

1.72_gcc-4.9.4
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Uniform Resource Identifiers (absolute and relative)

perl-want

0.29_gcc-4.9.4
 Click here to expand...

A generalisation of wantarray.

perl-www-robotrules

6.02_gcc-4.9.4
 Click here to expand...

Database of robots.txt-derived permissions

perl-xml-dom

1.46_gcc-4.9.4
 Click here to expand...

This module extends the XML::Parser module by Clark Cooper. The XML::Parser module is built on top of XML::Parser::Expat, which is a lower level interface to James Clark's expat library.

perl-xml-dom-xpath

0.14_gcc-4.9.4
 Click here to expand...

XML::DOM::XPath allows you to use XML::XPath methods to query a DOM. This is often much easier than relying only on getElementsByTagName.

perl-xml-filter-buffertext

1.01_gcc-4.9.4
 Click here to expand...

This is a very simple filter. One common cause of grief (and programmer error) is that XML parsers aren't required to provide character events in one chunk. They can, but are not forced to, and most don't. This filter does the trivial but oft-repeated task of putting all characters into a single event.

perl-xml-libxml

2.0201_gcc-4.9.4
 Click here to expand...

This module is an interface to libxml2, providing XML and HTML parsers with DOM, SAX and XMLReader interfaces, a large subset of DOM Layer 3 interface and a XML::XPath-like interface to XPath API of libxml2. The module is split into several packages which are not described in this section; unless stated otherwise, you only need to use XML::LibXML; in your programs.

perl-xml-namespacesupport

1.12_9_gcc-4.9.4
 Click here to expand...

This module offers a simple to process namespaced XML names (unames) from within any application that may need them. It also helps maintain a prefix to namespace URI map, and provides a number of basic checks.

perl-xml-parser

2.44_gcc-4.9.4
 Click here to expand...

XML::Parser - A perl module for parsing XML documents

perl-xml-quote

1.02_gcc-4.9.4
 Click here to expand...

This module provides functions to quote/dequote strings in 'xml'-way.

perl-xml-regexp

0.04_gcc-4.9.4
 Click here to expand...

This package contains regular expressions for the following XML tokens: BaseChar, Ideographic, Letter, Digit, Extender, CombiningChar, NameChar, EntityRef, CharRef, Reference, Name, NmToken, and AttValue.

perl-xml-sax

1.02_gcc-4.9.4
 Click here to expand...

XML::SAX is a SAX parser access API for Perl. It includes classes and APIs required for implementing SAX drivers, along with a factory class for returning any SAX parser installed on the user's system.

perl-xml-sax-base

1.09_gcc-4.9.4
 Click here to expand...

This module has a very simple task - to be a base class for PerlSAX drivers and filters. It's default behaviour is to pass the input directly to the output unchanged. It can be useful to use this module as a base class so you don't have to, for example, implement the characters() callback.

perl-xml-sax-writer

0.57_gcc-4.9.4
 Click here to expand...

A new XML Writer was needed to match the SAX2 effort because quite naturally no existing writer understood SAX2. My first intention had been to start patching XML::Handler::YAWriter as it had previously been my favourite writer in the SAX1 world.

perl-xml-twig

3.52_gcc-4.9.4
 Click here to expand...

This module provides a way to process XML documents. It is build on top of XML::Parser.

perl-xml-writer

0.625_gcc-4.9.4
 Click here to expand...

XML::Writer is a helper module for Perl programs that write an XML document. The module handles all escaping for attribute values and character data and constructs different types of markup, such as tags, comments, and processing instructions.

perl-xml-xpathengine

0.14_gcc-4.9.4
 Click here to expand...

This module provides an XPath engine, that can be re-used by other module/classes that implement trees.

perl-yaml

1.27_gcc-4.9.4
1.27_gcc-9.2.0

 Click here to expand...

This module has been released to CPAN as YAML::Old, and soon YAML.pm will be changed to just be a frontend interface module for all the various Perl YAML implementation modules, including YAML::Old

perl-yaml-libyaml

0.67_gcc-4.9.4
 Click here to expand...

Perl YAML Serialization using XS and libyaml

petsc

3.13.1_gcc-9.2.0
3.13.1_intel-19.0.5.281

 Click here to expand...

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

pixman

0.38.0_gcc-4.9.4
0.38.0_gcc-8.3.0
0.38.0_gcc-9.2.0
0.38.0_intel-19.0.5.281

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The Pixman package contains a library that provides low-level pixel manipulation features such as image compositing and trapezoid rasterization.

pkgconf

1.6.3_gcc-4.9.4
1.6.3_gcc-8.3.0
1.6.3_gcc-9.2.0
1.6.3_intel-19.0.5.281

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pkgconf is a program which helps to configure compiler and linker flags for development frameworks. It is similar to pkg-config from freedesktop.org, providing additional functionality while also maintaining compatibility.

poppler

0.79.0_gcc-8.3.0
0.79.0_gcc-9.2.0

 Click here to expand...

Poppler is a PDF rendering library based on the xpdf-3.0 code base.

poppler-data

0.4.9_gcc-8.3.0
0.4.9_gcc-9.2.0

 Click here to expand...

This package consists of encoding files for use with poppler. The encoding files are optional and poppler will automatically read them if they are present. When installed, the encoding files enables poppler to correctly render CJK and Cyrrilic properly. While poppler is licensed under the GPL, these encoding files have different license, and thus distributed separately.

postgresql

11.2_gcc-4.9.4
11.2_gcc-8.3.0
11.2_gcc-9.2.0
11.2_intel-19.0.5.281

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PostgreSQL is a powerful, open source object-relational database system. It has more than 15 years of active development and a proven architecture that has earned it a strong reputation for reliability, data integrity, and correctness.

proj

5.2.0_gcc-4.9.4
5.2.0_gcc-8.3.0
5.2.0_gcc-9.2.0
5.2.0_intel-19.0.5.281
6.2.0_gcc-4.9.4
6.2.0_gcc-8.3.0
6.2.0_gcc-9.2.0
6.2.0_intel-19.0.5.281

 Click here to expand...

PROJ is a generic coordinate transformation software, that transforms geospatial coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations.

protobuf

3.5.0_gcc-8.3.0
 Click here to expand...

Google's data interchange format.

py-absl-py

0.7.0_gcc-4.9.4
0.7.0_gcc-8.3.0
0.7.0_gcc-9.2.0
0.7.0_intel-19.0.5.281

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This repository is a collection of Python library code for building Python applications.

py-agate

1.6.1_gcc-4.9.4
1.6.1_gcc-8.3.0
1.6.1_gcc-9.2.0
1.6.1_intel-19.0.5.281

 Click here to expand...

agate is a Python data analysis library that is optimized for humans instead of machines. It is an alternative to numpy and pandas that solves real-world problems with readable code.

py-agate-dbf

0.2.1_gcc-4.9.4
0.2.1_gcc-8.3.0
0.2.1_gcc-9.2.0
0.2.1_intel-19.0.5.281

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agate-dbf adds read support for dbf files to agate.

py-agate-excel

0.2.3_gcc-4.9.4
0.2.3_gcc-8.3.0
0.2.3_gcc-9.2.0
0.2.3_intel-19.0.5.281

 Click here to expand...

agate-excel adds read support for Excel files (xls and xlsx) to agate.

py-agate-sql

0.5.4_gcc-4.9.4
0.5.4_gcc-8.3.0
0.5.4_gcc-9.2.0
0.5.4_intel-19.0.5.281

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agate-sql adds SQL read/write support to agate.

py-alabaster

0.7.12_gcc-4.9.4
0.7.12_gcc-8.3.0
0.7.12_gcc-9.2.0
0.7.12_intel-19.0.5.281

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Alabaster is a visually (c)lean, responsive, configurable theme for the Sphinx documentation system.

py-arviz

0.6.1_gcc-8.3.0
 Click here to expand...

ArviZ (pronounced 'AR-vees') is a Python package for exploratory analysis of Bayesian models. Includes functions for posterior analysis, model checking, comparison and diagnostics.

py-asn1crypto

0.22.0_gcc-4.9.4
0.22.0_gcc-8.3.0
0.22.0_gcc-9.2.0
0.22.0_intel-19.0.5.281

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Python ASN.1 library with a focus on performance and a pythonic API

py-astor

0.8.0_gcc-8.3.0
 Click here to expand...

astor is designed to allow easy manipulation of Python source via the AST.

py-atomicwrites

1.3.0_gcc-4.9.4
1.3.0_gcc-8.3.0
1.3.0_gcc-9.2.0
1.3.0_intel-19.0.5.281

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Atomic file writes.

py-attrs

19.2.0_gcc-4.9.4
19.2.0_gcc-8.3.0
19.2.0_gcc-9.2.0
19.2.0_intel-19.0.5.281

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Classes Without Boilerplate

py-audioread

2.1.8_gcc-4.9.4
2.1.8_gcc-8.3.0
2.1.8_gcc-9.2.0

 Click here to expand...

cross-library (GStreamer + Core Audio + MAD + FFmpeg) audio decoding for Python.

py-auxlib

0.0.43_gcc-4.9.4
0.0.43_gcc-8.3.0
0.0.43_gcc-9.2.0
0.0.43_intel-19.0.5.281

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Auxlib is an auxiliary library to the python standard library.

py-babel

2.7.0_gcc-4.9.4
2.7.0_gcc-8.3.0
2.7.0_gcc-9.2.0
2.7.0_intel-19.0.5.281

 Click here to expand...

Babel is an integrated collection of utilities that assist in internationalizing and localizing Python applications, with an emphasis on web-based applications.

py-backcall

0.1.0_gcc-4.9.4
0.1.0_gcc-8.3.0
0.1.0_gcc-9.2.0
0.1.0_intel-19.0.5.281

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Specifications for callback functions passed in to an API

py-backports-weakref

1.0.post1_gcc-4.9.4
1.0.post1_gcc-8.3.0
1.0.post1_gcc-9.2.0
1.0.post1_intel-19.0.5.281

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Backports of new features in Python's weakref module

py-basemap

1.2.0_gcc-4.9.4
1.2.0_gcc-8.3.0
1.2.0_gcc-9.2.0
1.2.0_intel-19.0.5.281

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The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python.

py-beautifulsoup4

4.8.0_gcc-4.9.4
4.8.0_gcc-8.3.0
4.8.0_gcc-9.2.0
4.8.0_intel-19.0.5.281

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Beautiful Soup is a Python library for pulling data out of HTML and XML files. It works with your favorite parser to provide idiomatic ways of navigating, searching, and modifying the parse tree.

py-biopython

1.73_gcc-4.9.4
1.73_gcc-8.3.0
1.73_gcc-9.2.0
1.73_intel-19.0.5.281

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A distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

py-bitarray

0.8.1_gcc-4.9.4
0.8.1_gcc-8.3.0
0.8.1_gcc-9.2.0
0.8.1_intel-19.0.5.281

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Efficient array of booleans - C extension

py-bleach

3.1.0_gcc-4.9.4
3.1.0_gcc-8.3.0
3.1.0_gcc-9.2.0
3.1.0_intel-19.0.5.281

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An easy allowlist-based HTML-sanitizing tool.

py-boto3

1.10.44_gcc-4.9.4
1.10.44_gcc-8.3.0
1.10.44_gcc-9.2.0
1.10.44_intel-19.0.5.281

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The AWS SDK for Python.

py-botocore

1.13.44_gcc-4.9.4
1.13.44_gcc-8.3.0
1.13.44_gcc-9.2.0
1.13.44_intel-19.0.5.281

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Low-level, data-driven core of boto 3.

py-bottleneck

1.2.1_gcc-4.9.4
1.2.1_gcc-8.3.0
1.2.1_gcc-9.2.0
1.2.1_intel-19.0.5.281

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A collection of fast NumPy array functions written in Cython.

py-bx-python

0.8.8_gcc-4.9.4
0.8.8_gcc-8.3.0
0.8.8_gcc-9.2.0
0.8.8_intel-19.0.5.281

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The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses.

py-certifi

2019.9.11_gcc-4.9.4
2019.9.11_gcc-8.3.0
2019.9.11_gcc-9.2.0
2019.9.11_intel-19.0.5.281

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Certifi: A carefully curated collection of Root Certificates for validating the trustworthiness of SSL certificates while verifying the identity of TLS hosts.

py-cffi

1.13.0_gcc-4.9.4
1.13.0_gcc-8.3.0
1.13.0_gcc-9.2.0
1.13.0_intel-19.0.5.281

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Foreign Function Interface for Python calling C code

py-cftime

1.0.3.4_gcc-4.9.4
1.0.3.4_gcc-8.3.0
1.0.3.4_gcc-9.2.0
1.0.3.4_intel-19.0.5.281

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Python library for decoding time units and variable values in a netCDF file conforming to the Climate and Forecasting (CF) netCDF conventions

py-chardet

3.0.4_gcc-4.9.4
3.0.4_gcc-8.3.0
3.0.4_gcc-9.2.0
3.0.4_intel-19.0.5.281

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Universal encoding detector for Python 2 and 3

py-click

7.0_gcc-4.9.4
7.0_gcc-8.3.0
7.0_gcc-9.2.0
7.0_intel-19.0.5.281

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A simple wrapper around optparse for powerful command line utilities.

py-cloudpickle

1.2.1_gcc-4.9.4
1.2.1_gcc-8.3.0
1.2.1_gcc-9.2.0
1.2.1_intel-19.0.5.281

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Extended pickling support for Python objects.

py-cnvkit

0.9.6_gcc-4.9.4
0.9.6_gcc-8.3.0
0.9.6_gcc-9.2.0
0.9.6_intel-19.0.5.281

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Copy number variation toolkit for high-throughput sequencing.

py-colorama

0.4.1_gcc-4.9.4
0.4.1_gcc-8.3.0
0.4.1_gcc-9.2.0
0.4.1_intel-19.0.5.281

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Cross-platform colored terminal text.

py-colormath

3.0.0_gcc-4.9.4
3.0.0_gcc-8.3.0
3.0.0_gcc-9.2.0
3.0.0_intel-19.0.5.281

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Color math and conversion library.

py-cryptography

2.3.1_gcc-4.9.4
2.3.1_gcc-8.3.0
2.3.1_gcc-9.2.0
2.3.1_intel-19.0.5.281

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cryptography is a package which provides cryptographic recipes and primitives to Python developers

py-csvkit

1.0.4_gcc-4.9.4
1.0.4_gcc-8.3.0
1.0.4_gcc-9.2.0
1.0.4_intel-19.0.5.281

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A library of utilities for working with CSV, the king of tabular file formats

py-cycler

0.10.0_gcc-4.9.4
0.10.0_gcc-8.3.0
0.10.0_gcc-9.2.0
0.10.0_intel-19.0.5.281

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Composable style cycles.

py-cython

0.29.13_gcc-4.9.4
0.29.13_gcc-8.3.0
0.29.13_gcc-9.2.0
0.29.13_intel-19.0.5.281

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The Cython compiler for writing C extensions for the Python language.

py-dask

1.1.2_gcc-4.9.4
1.1.2_gcc-8.3.0
1.1.2_gcc-9.2.0
1.1.2_intel-19.0.5.281

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Dask is a flexible parallel computing library for analytics.

py-dbfread

2.0.7_gcc-4.9.4
2.0.7_gcc-8.3.0
2.0.7_gcc-9.2.0
2.0.7_intel-19.0.5.281

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DBF is a file format used by databases such dBase, Visual FoxPro, and FoxBase+. This library reads DBF files and returns the data as native Python data types for further processing. It is primarily intended for batch jobs and one-off scripts.

py-decorator

4.4.0_gcc-4.9.4
4.4.0_gcc-8.3.0
4.4.0_gcc-9.2.0
4.4.0_intel-19.0.5.281

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The aim of the decorator module it to simplify the usage of decorators for the average programmer, and to popularize decorators by showing various non-trivial examples.

py-defusedxml

0.5.0_gcc-4.9.4
0.5.0_gcc-8.3.0
0.5.0_gcc-9.2.0
0.5.0_intel-19.0.5.281

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defusing XML bombs and other exploits

py-docopt

0.6.2_gcc-4.9.4
0.6.2_gcc-8.3.0
0.6.2_gcc-9.2.0
0.6.2_intel-19.0.5.281

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Command-line interface description language.

py-docutils

0.15.2_gcc-4.9.4
0.15.2_gcc-8.3.0
0.15.2_gcc-9.2.0
0.15.2_intel-19.0.5.281

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Docutils is an open-source text processing system for processing plaintext documentation into useful formats, such as HTML, LaTeX, man-pages, open-document or XML. It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get plaintext markup language.

py-entrypoints

0.3_gcc-4.9.4
0.3_gcc-8.3.0
0.3_gcc-9.2.0
0.3_intel-19.0.5.281

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Discover and load entry points from installed packages.

py-et-xmlfile

1.0.1_gcc-4.9.4
1.0.1_gcc-8.3.0
1.0.1_gcc-9.2.0
1.0.1_intel-19.0.5.281

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An implementation of lxml.xmlfile for the standard library.

py-fisher

0.1.9_gcc-9.2.0
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Simple, fast implementation of Fisher's exact test.

py-flask

1.1.1_gcc-4.9.4
1.1.1_gcc-8.3.0
1.1.1_gcc-9.2.0
1.1.1_intel-19.0.5.281

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A simple framework for building complex web applications.

py-future

0.17.1_gcc-4.9.4
0.17.1_gcc-8.3.0
0.17.1_gcc-9.2.0
0.17.1_intel-19.0.5.281

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Clean single-source support for Python 3 and 2

py-futures

3.0.5_gcc-4.9.4
3.0.5_gcc-8.3.0
3.0.5_gcc-9.2.0
3.0.5_intel-19.0.5.281

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Backport of the concurrent.futures package from Python 3.2

py-gast

0.2.2_gcc-8.3.0
0.3.2_gcc-8.3.0

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Python AST that abstracts the underlying Python version

py-google-pasta

0.1.8_gcc-8.3.0
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pasta is an AST-based Python refactoring library.

py-graphviz

0.10.1_gcc-4.9.4
0.10.1_gcc-8.3.0
0.10.1_gcc-9.2.0
0.10.1_intel-19.0.5.281

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Simple Python interface for Graphviz

py-grpcio

1.25.0_gcc-8.3.0
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HTTP/2-based RPC framework.

py-h5py

2.9.0_gcc-4.9.4
2.9.0_gcc-8.3.0
2.9.0_gcc-9.2.0
2.9.0_intel-19.0.5.281

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The h5py package provides both a high- and low-level interface to the HDF5 library from Python.

py-html5lib

1.0.1_gcc-4.9.4
1.0.1_gcc-8.3.0
1.0.1_gcc-9.2.0
1.0.1_intel-19.0.5.281

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HTML parser based on the WHATWG HTML specification.

py-htseq

0.11.2_gcc-4.9.4
0.11.2_gcc-8.3.0
0.11.2_gcc-9.2.0
0.11.2_intel-19.0.5.281

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HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

py-hypothesis

4.41.2_gcc-4.9.4
4.41.2_gcc-8.3.0
4.41.2_gcc-9.2.0
4.41.2_intel-19.0.5.281

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A library for property based testing.

py-idna

2.8_gcc-4.9.4
2.8_gcc-8.3.0
2.8_gcc-9.2.0
2.8_intel-19.0.5.281

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Internationalized Domain Names for Python (IDNA 2008 and UTS #46)

py-imagesize

1.1.0_gcc-4.9.4
1.1.0_gcc-8.3.0
1.1.0_gcc-9.2.0
1.1.0_intel-19.0.5.281

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Parses image file headers and returns image size. Supports PNG, JPEG, JPEG2000, and GIF image file formats.

py-importlib-metadata

1.2.0_gcc-4.9.4
1.2.0_gcc-8.3.0
1.2.0_gcc-9.2.0
1.2.0_intel-19.0.5.281

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Read metadata from Python packages.

py-ipykernel

5.1.0_gcc-4.9.4
5.1.0_gcc-8.3.0
5.1.0_gcc-9.2.0
5.1.0_intel-19.0.5.281

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IPython Kernel for Jupyter

py-ipython

7.3.0_gcc-4.9.4
7.3.0_gcc-8.3.0
7.3.0_gcc-9.2.0
7.3.0_intel-19.0.5.281

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IPython provides a rich toolkit to help you make the most out of using Python interactively.

py-ipython-genutils

0.2.0_gcc-4.9.4
0.2.0_gcc-8.3.0
0.2.0_gcc-9.2.0
0.2.0_intel-19.0.5.281

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Vestigial utilities from IPython

py-ipywidgets

7.5.1_gcc-4.9.4
7.5.1_gcc-8.3.0
7.5.1_gcc-9.2.0
7.5.1_intel-19.0.5.281

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IPython widgets for the Jupyter Notebook

py-isodate

0.6.0_gcc-4.9.4
0.6.0_gcc-8.3.0
0.6.0_gcc-9.2.0
0.6.0_intel-19.0.5.281

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This module implements ISO 8601 date, time and duration parsing. The implementation follows ISO8601:2004 standard, and implements only date/time representations mentioned in the standard. If something is not mentioned there, then it is treated as non existent, and not as an allowed option.

py-itsdangerous

1.1.0_gcc-4.9.4
1.1.0_gcc-8.3.0
1.1.0_gcc-9.2.0
1.1.0_intel-19.0.5.281

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Various helpers to pass trusted data to untrusted environments.

py-jdcal

1.3_gcc-4.9.4
1.3_gcc-8.3.0
1.3_gcc-9.2.0
1.3_intel-19.0.5.281

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Julian dates from proleptic Gregorian and Julian calendars

py-jinja2

2.10.3_gcc-4.9.4
2.10.3_gcc-8.3.0
2.10.3_gcc-9.2.0
2.10.3_intel-19.0.5.281

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Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.

py-jmespath

0.9.4_gcc-4.9.4
0.9.4_gcc-8.3.0
0.9.4_gcc-9.2.0
0.9.4_intel-19.0.5.281

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JSON Matching Expressions.

py-joblib

0.14.0_gcc-4.9.4
0.14.0_gcc-8.3.0
0.14.0_gcc-9.2.0
0.14.0_intel-19.0.5.281

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Python function as pipeline jobs

py-jsonschema

2.6.0_gcc-4.9.4
2.6.0_gcc-8.3.0
2.6.0_gcc-9.2.0
2.6.0_intel-19.0.5.281

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Jsonschema: An(other) implementation of JSON Schema for Python.

py-jupyter

1.0.0_gcc-4.9.4
1.0.0_gcc-8.3.0
1.0.0_gcc-9.2.0
1.0.0_intel-19.0.5.281

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Jupyter metapackage. Install all the Jupyter components in one go.

py-jupyter-client

5.3.4_gcc-4.9.4
5.3.4_gcc-8.3.0
5.3.4_gcc-9.2.0
5.3.4_intel-19.0.5.281

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Jupyter protocol client APIs

py-jupyter-console

6.1.0_gcc-4.9.4
6.1.0_gcc-8.3.0
6.1.0_gcc-9.2.0
6.1.0_intel-19.0.5.281

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Jupyter Terminal Console

py-jupyter-core

4.6.0_gcc-4.9.4
4.6.0_gcc-8.3.0
4.6.0_gcc-9.2.0
4.6.0_intel-19.0.5.281

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Core Jupyter functionality

py-keras

2.2.4_gcc-8.3.0
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Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.

py-keras-applications

1.0.8_gcc-8.3.0
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Sample Deep Learning application in Keras. Keras depends on this package to run properly.

py-keras-preprocessing

1.1.0_gcc-8.3.0
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Utilities for working with image data, text data, and sequence data.

py-kiwisolver

1.1.0_gcc-4.9.4
1.1.0_gcc-8.3.0
1.1.0_gcc-9.2.0
1.1.0_intel-19.0.5.281

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A fast implementation of the Cassowary constraint solver

py-leather

0.3.3_gcc-4.9.4
0.3.3_gcc-8.3.0
0.3.3_gcc-9.2.0
0.3.3_intel-19.0.5.281

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Leather is the Python charting library for those who need charts now and don't care if they're perfect.

py-librosa

0.7.2_gcc-4.9.4
0.7.2_gcc-8.3.0
0.7.2_gcc-9.2.0

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A python package for music and audio analysis.

py-llvmlite

0.31.0_gcc-4.9.4
0.31.0_gcc-8.3.0
0.31.0_gcc-9.2.0

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A lightweight LLVM python binding for writing JIT compilers

py-locket

0.2.0_gcc-4.9.4
0.2.0_gcc-8.3.0
0.2.0_gcc-9.2.0
0.2.0_intel-19.0.5.281

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File-based locks for Python for Linux and Windows.

py-lzstring

1.0.3_gcc-4.9.4
1.0.3_gcc-8.3.0
1.0.3_gcc-9.2.0
1.0.3_intel-19.0.5.281

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lz-string for python.

py-mako

1.0.4_gcc-8.3.0
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A super-fast templating language that borrows the best ideas from the existing templating languages.

py-markdown

3.1.1_gcc-4.9.4
3.1.1_gcc-8.3.0
3.1.1_gcc-9.2.0
3.1.1_intel-19.0.5.281

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This is a Python implementation of John Gruber's Markdown. It is almost completely compliant with the reference implementation, though there are a few very minor differences. See John's Syntax Documentation for the syntax rules.

py-markupsafe

1.1.1_gcc-4.9.4
1.1.1_gcc-8.3.0
1.1.1_gcc-9.2.0
1.1.1_intel-19.0.5.281

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MarkupSafe is a library for Python that implements a unicode string that is aware of HTML escaping rules and can be used to implement automatic string escaping. It is used by Jinja 2, the Mako templating engine, the Pylons web framework and many more.

py-matplotlib

2.2.3_gcc-4.9.4
2.2.3_gcc-8.3.0
2.2.3_gcc-9.2.0
2.2.3_intel-19.0.5.281
3.1.2_gcc-4.9.4
3.1.2_gcc-8.3.0
3.1.2_gcc-9.2.0
3.1.2_intel-19.0.5.281

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matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.

py-misopy

0.5.4_gcc-4.9.4
0.5.4_gcc-8.3.0
0.5.4_gcc-9.2.0
0.5.4_intel-19.0.5.281

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MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.

py-mistune

0.8.4_gcc-4.9.4
0.8.4_gcc-8.3.0
0.8.4_gcc-9.2.0
0.8.4_intel-19.0.5.281

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Python markdown parser

py-mock

3.0.5_gcc-4.9.4
3.0.5_gcc-8.3.0
3.0.5_gcc-9.2.0
3.0.5_intel-19.0.5.281

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mock is a library for testing in Python. It allows you to replace parts of your system under test with mock objects and make assertions about how they have been used.

py-more-itertools

7.2.0_gcc-4.9.4
7.2.0_gcc-8.3.0
7.2.0_gcc-9.2.0
7.2.0_intel-19.0.5.281

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Additions to the standard Python itertools package.

py-mpi4py

3.0.3_gcc-4.9.4
3.0.3_gcc-8.3.0
3.0.3_gcc-9.2.0
3.0.3_intel-19.0.5.281

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This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.

py-mpmath

1.1.0_gcc-4.9.4
1.1.0_gcc-8.3.0
1.1.0_gcc-9.2.0
1.1.0_intel-19.0.5.281

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A Python library for arbitrary-precision floating-point arithmetic.

py-multiqc

1.7_gcc-4.9.4
1.7_gcc-8.3.0
1.7_gcc-9.2.0
1.7_intel-19.0.5.281

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MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It is written in Python and contains modules for a large number of common bioinformatics tools.

py-nbconvert

5.6.0_gcc-4.9.4
5.6.0_gcc-8.3.0
5.6.0_gcc-9.2.0
5.6.0_intel-19.0.5.281

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Jupyter Notebook Conversion

py-nbformat

4.4.0_gcc-4.9.4
4.4.0_gcc-8.3.0
4.4.0_gcc-9.2.0
4.4.0_intel-19.0.5.281

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The Jupyter Notebook format

py-netcdf4

1.4.2_gcc-4.9.4
1.4.2_gcc-8.3.0
1.4.2_gcc-9.2.0
1.4.2_intel-19.0.5.281

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Python interface to the netCDF Library.

py-networkx

2.2_gcc-4.9.4
2.2_gcc-8.3.0
2.2_gcc-9.2.0
2.2_intel-19.0.5.281

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NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

py-nose

1.3.7_gcc-8.3.0
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nose extends the test loading and running features of unittest, making it easier to write, find and run tests.

py-notebook

6.0.1_gcc-4.9.4
6.0.1_gcc-8.3.0
6.0.1_gcc-9.2.0
6.0.1_intel-19.0.5.281

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Jupyter Interactive Notebook

py-numba

0.48.0_gcc-4.9.4
0.48.0_gcc-8.3.0
0.48.0_gcc-9.2.0

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NumPy aware dynamic Python compiler using LLVM

py-numexpr

2.7.0_gcc-4.9.4
2.7.0_gcc-8.3.0
2.7.0_gcc-9.2.0
2.7.0_intel-19.0.5.281

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Fast numerical expression evaluator for NumPy

py-numpy

1.18.0_gcc-4.9.4
1.18.0_gcc-8.3.0
1.18.0_gcc-9.2.0
1.18.0_intel-19.0.5.281

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NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities

py-numpydoc

0.6.0_gcc-4.9.4
0.6.0_gcc-8.3.0
0.6.0_gcc-9.2.0
0.6.0_intel-19.0.5.281

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numpydoc - Numpy's Sphinx extensions

py-openpyxl

2.4.5_gcc-4.9.4
2.4.5_gcc-8.3.0
2.4.5_gcc-9.2.0
2.4.5_intel-19.0.5.281

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A Python library to read/write Excel 2010 xlsx/xlsm files

py-opt-einsum

3.1.0_gcc-8.3.0
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Optimized Einsum: A tensor contraction order optimizer.

py-ordereddict

1.1_gcc-4.9.4
1.1_gcc-8.3.0
1.1_gcc-9.2.0
1.1_intel-19.0.5.281

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A drop-in substitute for Py2.7's new collections. OrderedDict that works in Python 2.4-2.6.

py-packaging

19.2_gcc-4.9.4
19.2_gcc-8.3.0
19.2_gcc-9.2.0
19.2_intel-19.0.5.281

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Core utilities for Python packages.

py-pandas

0.24.2_gcc-4.9.4
0.24.2_gcc-8.3.0
0.24.2_gcc-9.2.0
0.24.2_intel-19.0.5.281
0.25.1_gcc-4.9.4
0.25.1_gcc-8.3.0
0.25.1_gcc-9.2.0
0.25.1_intel-19.0.5.281

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pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with relational or labeled data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. Additionally, it has the broader goal of becoming the most powerful and flexible open source data analysis / manipulation tool available in any language.

py-pandocfilters

1.4.2_gcc-4.9.4
1.4.2_gcc-8.3.0
1.4.2_gcc-9.2.0
1.4.2_intel-19.0.5.281

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A python module for writing pandoc filters

py-parsedatetime

2.5_gcc-4.9.4
2.5_gcc-8.3.0
2.5_gcc-9.2.0
2.5_intel-19.0.5.281

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Parse human-readable date/time strings.

py-partd

0.3.8_gcc-4.9.4
0.3.8_gcc-8.3.0
0.3.8_gcc-9.2.0
0.3.8_intel-19.0.5.281

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Key-value byte store with appendable values.

py-patsy

0.5.1_gcc-4.9.4
0.5.1_gcc-8.3.0
0.5.1_gcc-9.2.0
0.5.1_intel-19.0.5.281

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A Python package for describing statistical models and for building design matrices.

py-pexpect

4.6.0_gcc-4.9.4
4.6.0_gcc-8.3.0
4.6.0_gcc-9.2.0
4.6.0_intel-19.0.5.281

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Pexpect allows easy control of interactive console applications.

py-pickleshare

0.7.4_gcc-4.9.4
0.7.4_gcc-8.3.0
0.7.4_gcc-9.2.0
0.7.4_intel-19.0.5.281

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Tiny 'shelve'-like database with concurrency support

py-pillow

6.2.0_gcc-4.9.4
6.2.0_gcc-8.3.0
6.2.0_gcc-9.2.0
6.2.0_intel-19.0.5.281

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Pillow is a fork of the Python Imaging Library (PIL). It adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.

py-pip

19.3_gcc-4.9.4
19.3_gcc-8.3.0
19.3_gcc-9.2.0
19.3_intel-19.0.5.281

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The PyPA recommended tool for installing Python packages.

py-pkgconfig

1.5.1_gcc-4.9.4
1.5.1_gcc-8.3.0
1.5.1_gcc-9.2.0
1.5.1_intel-19.0.5.281

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Interface Python with pkg-config.

py-pluggy

0.13.0_gcc-4.9.4
0.13.0_gcc-8.3.0
0.13.0_gcc-9.2.0
0.13.0_intel-19.0.5.281

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Plugin and hook calling mechanisms for python.

py-pomegranate

0.12.0_gcc-4.9.4
0.12.0_gcc-8.3.0
0.12.0_gcc-9.2.0
0.12.0_intel-19.0.5.281

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Fast, flexible and easy to use probabilistic modelling in Python.

py-prometheus-client

0.7.1_gcc-4.9.4
0.7.1_gcc-8.3.0
0.7.1_gcc-9.2.0
0.7.1_intel-19.0.5.281

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Prometheus instrumentation library for Python applications.

py-prompt-toolkit

2.0.9_gcc-4.9.4
2.0.9_gcc-8.3.0
2.0.9_gcc-9.2.0
2.0.9_intel-19.0.5.281

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Library for building powerful interactive command lines in Python

py-protobuf

3.11.0_gcc-4.9.4
3.11.0_gcc-8.3.0
3.11.0_gcc-9.2.0
3.11.0_intel-19.0.5.281

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Protocol buffers are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data - think XML, but smaller, faster, and simpler. You define how you want your data to be structured once, then you can use special generated source code to easily write and read your structured data to and from a variety of data streams and using a variety of languages.

py-psycopg2

2.7.5_gcc-4.9.4
2.7.5_gcc-8.3.0
2.7.5_gcc-9.2.0
2.7.5_intel-19.0.5.281

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Python interface to PostgreSQL databases

py-ptyprocess

0.5.1_gcc-4.9.4
0.5.1_gcc-8.3.0
0.5.1_gcc-9.2.0
0.5.1_intel-19.0.5.281

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Run a subprocess in a pseudo terminal

py-py

1.8.0_gcc-4.9.4
1.8.0_gcc-8.3.0
1.8.0_gcc-9.2.0
1.8.0_intel-19.0.5.281

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Library with cross-python path, ini-parsing, io, code, log facilities

py-pyasn1

0.4.6_gcc-4.9.4
0.4.6_gcc-8.3.0
0.4.6_gcc-9.2.0
0.4.6_intel-19.0.5.281

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Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208).

py-pybigwig

0.3.12_gcc-4.9.4
0.3.12_gcc-8.3.0
0.3.12_gcc-9.2.0
0.3.12_intel-19.0.5.281

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A package for accessing bigWig files using libBigWig.

py-pybind11

2.4.3_gcc-8.3.0
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pybind11 – Seamless operability between C++11 and Python.

py-pycifrw

4.4.1_gcc-4.9.4
4.4.1_gcc-8.3.0
4.4.1_gcc-9.2.0
4.4.1_intel-19.0.5.281

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Python library for interacting with Crystallographic Information Framework (CIF) files.

py-pycparser

2.19_gcc-4.9.4
2.19_gcc-8.3.0
2.19_gcc-9.2.0
2.19_intel-19.0.5.281

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A complete parser of the C language, written in pure python.

py-pydot

1.4.1_gcc-4.9.4
1.4.1_gcc-8.3.0
1.4.1_gcc-9.2.0
1.4.1_intel-19.0.5.281

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Python interface to Graphviz's Dot language

py-pyfaidx

0.5.5.2_gcc-4.9.4
0.5.5.2_gcc-8.3.0
0.5.5.2_gcc-9.2.0
0.5.5.2_intel-19.0.5.281

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pyfaidx: efficient pythonic random access to fasta subsequences

py-pygments

2.4.2_gcc-4.9.4
2.4.2_gcc-8.3.0
2.4.2_gcc-9.2.0
2.4.2_intel-19.0.5.281

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Pygments is a syntax highlighting package written in Python.

py-pygpu

0.7.5_gcc-8.3.0
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Python packge for the libgpuarray C library.

py-pymc3

3.8_gcc-8.3.0
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PyMC3 is a Python package for Bayesian statistical modeling and Probabilistic Machine Learning focusing on advanced Markov chain Monte Carlo (MCMC) and variational inference (VI) algorithms. Its flexibility and extensibility make it applicable to a large suite of problems.

py-pymysql

0.9.2_gcc-4.9.4
0.9.2_gcc-8.3.0
0.9.2_gcc-9.2.0
0.9.2_intel-19.0.5.281

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Pure-Python MySQL client library

py-pyparsing

2.4.2_gcc-4.9.4
2.4.2_gcc-8.3.0
2.4.2_gcc-9.2.0
2.4.2_intel-19.0.5.281

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A Python Parsing Module.

py-pyproj

1.9.6_gcc-4.9.4
1.9.6_gcc-8.3.0
1.9.6_gcc-9.2.0
1.9.6_intel-19.0.5.281

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Python interface to the PROJ.4 Library.

py-pyqt5

5.13.0_gcc-4.9.4
5.13.0_gcc-8.3.0
5.13.0_gcc-9.2.0
5.13.0_intel-19.0.5.281

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PyQt is a set of Python v2 and v3 bindings for The Qt Company's Qt application framework and runs on all platforms supported by Qt including Windows, OS X, Linux, iOS and Android. PyQt5 supports Qt v5.

py-pysam

0.15.2_gcc-4.9.4
0.15.2_gcc-8.3.0
0.15.2_gcc-9.2.0
0.15.2_intel-19.0.5.281

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A python module for reading, manipulating and writing genomic data sets.

py-pyshp

1.2.12_gcc-4.9.4
1.2.12_gcc-8.3.0
1.2.12_gcc-9.2.0
1.2.12_intel-19.0.5.281

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The Python Shapefile Library (pyshp) reads and writes ESRI Shapefiles in pure Python.

py-pytest

5.2.1_gcc-4.9.4
5.2.1_gcc-8.3.0
5.2.1_gcc-9.2.0
5.2.1_intel-19.0.5.281

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pytest: simple powerful testing with Python.

py-python-dateutil

2.8.0_gcc-4.9.4
2.8.0_gcc-8.3.0
2.8.0_gcc-9.2.0
2.8.0_intel-19.0.5.281

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Extensions to the standard Python datetime module.

py-python-slugify

4.0.0_gcc-4.9.4
4.0.0_gcc-8.3.0
4.0.0_gcc-9.2.0
4.0.0_intel-19.0.5.281

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A Python Slugify application that handles Unicode

py-pytimeparse

1.1.8_gcc-4.9.4
1.1.8_gcc-8.3.0
1.1.8_gcc-9.2.0
1.1.8_intel-19.0.5.281

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A small Python library to parse various kinds of time expressions.

py-pytz

2019.3_gcc-4.9.4
2019.3_gcc-8.3.0
2019.3_gcc-9.2.0
2019.3_intel-19.0.5.281

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World timezone definitions, modern and historical.

py-pyvcf

0.6.0_gcc-4.9.4
0.6.0_gcc-8.3.0
0.6.0_gcc-9.2.0
0.6.0_intel-19.0.5.281

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A Variant Call Format reader for Python

py-pywavelets

0.5.2_gcc-4.9.4
0.5.2_gcc-8.3.0
0.5.2_gcc-9.2.0
0.5.2_intel-19.0.5.281

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PyWavelets is a free Open Source library for wavelet transforms in Python

py-pyyaml

5.1.2_gcc-4.9.4
5.1.2_gcc-8.3.0
5.1.2_gcc-9.2.0
5.1.2_intel-19.0.5.281

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PyYAML is a YAML parser and emitter for Python.

py-pyzmq

18.1.0_gcc-4.9.4
18.1.0_gcc-8.3.0
18.1.0_gcc-9.2.0
18.1.0_intel-19.0.5.281

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PyZMQ: Python bindings for zeromq.

py-qtconsole

4.5.1_gcc-4.9.4
4.5.1_gcc-8.3.0
4.5.1_gcc-9.2.0
4.5.1_intel-19.0.5.281

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Jupyter Qt console

py-reportlab

3.4.0_gcc-4.9.4
3.4.0_gcc-8.3.0
3.4.0_gcc-9.2.0
3.4.0_intel-19.0.5.281

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The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics.

py-requests

2.22.0_gcc-4.9.4
2.22.0_gcc-8.3.0
2.22.0_gcc-9.2.0
2.22.0_intel-19.0.5.281

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Python HTTP for Humans.

py-resampy

0.2.2_gcc-4.9.4
0.2.2_gcc-8.3.0
0.2.2_gcc-9.2.0

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Efficient sample rate conversion in python

py-rpy2

3.0.0_gcc-4.9.4
3.0.0_gcc-8.3.0
3.0.0_gcc-9.2.0
3.0.0_intel-19.0.5.281

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rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.

py-rsa

3.4.2_gcc-4.9.4
3.4.2_gcc-8.3.0
3.4.2_gcc-9.2.0
3.4.2_intel-19.0.5.281

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Pure-Python RSA implementation

py-rseqc

3.0.1_gcc-4.9.4
3.0.1_gcc-8.3.0
3.0.1_gcc-9.2.0
3.0.1_intel-19.0.5.281

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RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.

py-ruamel-yaml

0.16.5_gcc-4.9.4
0.16.5_gcc-8.3.0
0.16.5_gcc-9.2.0
0.16.5_intel-19.0.5.281

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a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order

py-s3transfer

0.2.1_gcc-4.9.4
0.2.1_gcc-8.3.0
0.2.1_gcc-9.2.0
0.2.1_intel-19.0.5.281

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S3transfer is a Python library for managing Amazon S3 transfers.

py-scikit-build

0.10.0_gcc-4.9.4
0.10.0_gcc-8.3.0
0.10.0_gcc-9.2.0
0.10.0_intel-19.0.5.281

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scikit-build is an improved build system generator for CPython C/C++/Fortran/Cython extensions. It provides better support for additional compilers, build systems, cross compilation, and locating dependencies and their associated build requirements.

py-scikit-image

0.14.2_gcc-4.9.4
0.14.2_gcc-8.3.0
0.14.2_gcc-9.2.0
0.14.2_intel-19.0.5.281

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Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.

py-scikit-learn

0.22_gcc-4.9.4
0.22_gcc-8.3.0
0.22_gcc-9.2.0
0.22_intel-19.0.5.281

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A set of python modules for machine learning and data mining.

py-scikit-optimize

0.5.2_gcc-4.9.4
0.5.2_gcc-8.3.0
0.5.2_gcc-9.2.0
0.5.2_intel-19.0.5.281

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Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. It implements several methods for sequential model-based optimization. skopt aims to be accessible and easy to use in many contexts.

py-scipy

1.4.1_gcc-4.9.4
1.4.1_gcc-8.3.0
1.4.1_gcc-9.2.0
1.4.1_intel-19.0.5.281

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SciPy (pronounced 'Sigh Pie') is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.

py-send2trash

1.5.0_gcc-4.9.4
1.5.0_gcc-8.3.0
1.5.0_gcc-9.2.0
1.5.0_intel-19.0.5.281

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Python library to send files to Trash/Recycle on all platforms.

py-setuptools

41.4.0_gcc-4.9.4
41.4.0_gcc-8.3.0
41.4.0_gcc-9.2.0
41.4.0_intel-19.0.5.281

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A Python utility that aids in the process of downloading, building, upgrading, installing, and uninstalling Python packages.

py-simplegeneric

0.8.1_gcc-4.9.4
0.8.1_gcc-8.3.0
0.8.1_gcc-9.2.0
0.8.1_intel-19.0.5.281

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Simple generic functions (similar to Python's own len(), pickle.dump(), etc.)

py-simplejson

3.10.0_gcc-4.9.4
3.10.0_gcc-8.3.0
3.10.0_gcc-9.2.0
3.10.0_intel-19.0.5.281

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Simplejson is a simple, fast, extensible JSON encoder/decoder for Python

py-six

1.12.0_gcc-4.9.4
1.12.0_gcc-8.3.0
1.12.0_gcc-9.2.0
1.12.0_intel-19.0.5.281

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Python 2 and 3 compatibility utilities.

py-snowballstemmer

2.0.0_gcc-4.9.4
2.0.0_gcc-8.3.0
2.0.0_gcc-9.2.0
2.0.0_intel-19.0.5.281

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This package provides 16 stemmer algorithms (15 + Poerter English stemmer) generated from Snowball algorithms.

py-soundfile

0.10.3.post1_gcc-4.9.4
0.10.3.post1_gcc-8.3.0
0.10.3.post1_gcc-9.2.0

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SoundFile is an audio library based on libsndfile, CFFI and NumPy.

py-soupsieve

1.9.3_gcc-4.9.4
1.9.3_gcc-8.3.0
1.9.3_gcc-9.2.0
1.9.3_intel-19.0.5.281

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A modern CSS selector implementation for Beautiful Soup.

py-spectra

0.0.11_gcc-4.9.4
0.0.11_gcc-8.3.0
0.0.11_gcc-9.2.0
0.0.11_intel-19.0.5.281

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Color scales and color conversion made easy for Python.

py-sphinx

2.2.0_gcc-4.9.4
2.2.0_gcc-8.3.0
2.2.0_gcc-9.2.0
2.2.0_intel-19.0.5.281

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Sphinx Documentation Generator.

py-sphinxcontrib-applehelp

1.0.1_gcc-4.9.4
1.0.1_gcc-8.3.0
1.0.1_gcc-9.2.0
1.0.1_intel-19.0.5.281

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sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books.

py-sphinxcontrib-devhelp

1.0.1_gcc-4.9.4
1.0.1_gcc-8.3.0
1.0.1_gcc-9.2.0
1.0.1_intel-19.0.5.281

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sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document.

py-sphinxcontrib-htmlhelp

1.0.2_gcc-4.9.4
1.0.2_gcc-8.3.0
1.0.2_gcc-9.2.0
1.0.2_intel-19.0.5.281

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sphinxcontrib-htmlhelp is a sphinx extension which outputs htmlhelp document.

py-sphinxcontrib-jsmath

1.0.1_gcc-4.9.4
1.0.1_gcc-8.3.0
1.0.1_gcc-9.2.0
1.0.1_intel-19.0.5.281

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A sphinx extension which renders display math in HTML via JavaScript.

py-sphinxcontrib-qthelp

1.0.2_gcc-4.9.4
1.0.2_gcc-8.3.0
1.0.2_gcc-9.2.0
1.0.2_intel-19.0.5.281

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sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document.

py-sphinxcontrib-serializinghtml

1.1.3_gcc-4.9.4
1.1.3_gcc-8.3.0
1.1.3_gcc-9.2.0
1.1.3_intel-19.0.5.281

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sphinxcontrib-serializinghtml is a sphinx extension which outputs 'serialized' HTML files (json and pickle).

py-sqlalchemy

1.3.9_gcc-4.9.4
1.3.9_gcc-8.3.0
1.3.9_gcc-9.2.0
1.3.9_intel-19.0.5.281

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The Python SQL Toolkit and Object Relational Mapper

py-sympy

1.3_gcc-4.9.4
1.3_gcc-8.3.0
1.3_gcc-9.2.0
1.3_intel-19.0.5.281

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SymPy is a Python library for symbolic mathematics.

py-tables

3.6.1_gcc-4.9.4
3.6.1_gcc-8.3.0
3.6.1_gcc-9.2.0
3.6.1_intel-19.0.5.281

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PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.

py-tensorflow

1.14.0_gcc-8.3.0
2.1.0_gcc-8.3.0

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TensorFlow is an Open Source Software Library for Machine Intelligence

py-termcolor

1.1.0_gcc-8.3.0
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ANSII Color formatting for output in terminal.

py-terminado

0.8.1_gcc-4.9.4
0.8.1_gcc-8.3.0
0.8.1_gcc-9.2.0
0.8.1_intel-19.0.5.281

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Terminals served to term.js using Tornado websockets

py-testpath

0.4.2_gcc-4.9.4
0.4.2_gcc-8.3.0
0.4.2_gcc-9.2.0
0.4.2_intel-19.0.5.281

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Testpath is a collection of utilities for Python code working with files and commands.

py-text-unidecode

1.3_gcc-4.9.4
1.3_gcc-8.3.0
1.3_gcc-9.2.0
1.3_intel-19.0.5.281

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text-unidecode is the most basic port of the Text::Unidecode Perl library.

py-theano

1.0.4_gcc-8.3.0
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Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs.

python

3.7.4_gcc-4.9.4
3.7.4_gcc-8.3.0
3.7.4_gcc-9.2.0
3.7.4_intel-19.0.5.281

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The Python programming language.

py-toolz

0.9.0_gcc-4.9.4
0.9.0_gcc-8.3.0
0.9.0_gcc-9.2.0
0.9.0_intel-19.0.5.281

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A set of utility functions for iterators, functions, and dictionaries

py-torch

1.4.0_gcc-8.3.0
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Tensors and Dynamic neural networks in Python with strong GPU acceleration.

py-torchvision

0.5.0_gcc-8.3.0
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The torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision.

py-tornado

6.0.3_gcc-4.9.4
6.0.3_gcc-8.3.0
6.0.3_gcc-9.2.0
6.0.3_intel-19.0.5.281

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Tornado is a Python web framework and asynchronous networking library.

py-tqdm

4.36.1_gcc-4.9.4
4.36.1_gcc-8.3.0
4.36.1_gcc-9.2.0
4.36.1_intel-19.0.5.281

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A Fast, Extensible Progress Meter

py-traitlets

4.3.3_gcc-4.9.4
4.3.3_gcc-8.3.0
4.3.3_gcc-9.2.0
4.3.3_intel-19.0.5.281

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Traitlets Python config system

py-twisted

15.4.0_gcc-4.9.4
15.4.0_gcc-8.3.0
15.4.0_gcc-9.2.0
15.4.0_intel-19.0.5.281

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An asynchronous networking framework written in Python

py-typing

3.7.4.1_gcc-4.9.4
3.7.4.1_gcc-8.3.0
3.7.4.1_gcc-9.2.0
3.7.4.1_intel-19.0.5.281

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This is a backport of the standard library typing module to Python versions older than 3.6.

py-urllib3

1.25.6_gcc-4.9.4
1.25.6_gcc-8.3.0
1.25.6_gcc-9.2.0
1.25.6_intel-19.0.5.281

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HTTP library with thread-safe connection pooling, file post, and more.

py-vcversioner

2.16.0.0_gcc-4.9.4
2.16.0.0_gcc-8.3.0
2.16.0.0_gcc-9.2.0
2.16.0.0_intel-19.0.5.281

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Vcversioner: Take version numbers from version control.

py-virtualenv

16.7.6_gcc-4.9.4
16.7.6_gcc-8.3.0
16.7.6_gcc-9.2.0
16.7.6_intel-19.0.5.281

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virtualenv is a tool to create isolated Python environments.

py-wcwidth

0.1.7_gcc-4.9.4
0.1.7_gcc-8.3.0
0.1.7_gcc-9.2.0
0.1.7_intel-19.0.5.281

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Measures number of Terminal column cells of wide-character codes

py-webencodings

0.5.1_gcc-4.9.4
0.5.1_gcc-8.3.0
0.5.1_gcc-9.2.0
0.5.1_intel-19.0.5.281

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This is a Python implementation of the WHATWG Encoding standard.

py-werkzeug

0.16.0_gcc-4.9.4
0.16.0_gcc-8.3.0
0.16.0_gcc-9.2.0
0.16.0_intel-19.0.5.281

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The Swiss Army knife of Python web development

py-wheel

0.33.1_gcc-4.9.4
0.33.1_gcc-8.3.0
0.33.1_gcc-9.2.0
0.33.1_intel-19.0.5.281

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A built-package format for Python.

py-widgetsnbextension

3.5.1_gcc-4.9.4
3.5.1_gcc-8.3.0
3.5.1_gcc-9.2.0
3.5.1_intel-19.0.5.281

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IPython HTML widgets for Jupyter

py-wrapt

1.11.2_gcc-8.3.0
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Module for decorators, wrappers and monkey patching.

py-xarray

0.14.0_gcc-4.9.4
0.14.0_gcc-8.3.0
0.14.0_gcc-9.2.0
0.14.0_intel-19.0.5.281

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N-D labeled arrays and datasets in Python

py-xlrd

0.9.4_gcc-4.9.4
0.9.4_gcc-8.3.0
0.9.4_gcc-9.2.0
0.9.4_intel-19.0.5.281

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Library for developers to extract data from Microsoft Excel (tm) spreadsheet files

py-youtube-dl

2020.3.24_gcc-4.9.4
2020.3.24_gcc-8.3.0
2020.3.24_gcc-9.2.0

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Command-line program to download videos from YouTube.com and other video sites.

py-zipp

0.6.0_gcc-4.9.4
0.6.0_gcc-8.3.0
0.6.0_gcc-9.2.0
0.6.0_intel-19.0.5.281

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Backport of pathlib-compatible object wrapper for zip files.

qt

5.13.1_gcc-4.9.4
5.13.1_gcc-8.3.0
5.13.1_gcc-9.2.0
5.13.1_intel-19.0.5.281

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Qt is a comprehensive cross-platform C++ application framework.

quantum-espresso

6.5_intel-19.0.5.281
6.5_intel-19.0.5.281-hdf5

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Quantum-ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

r

3.6.2_gcc-4.9.4
3.6.2_gcc-8.3.0
3.6.2_gcc-9.2.0
3.6.2_intel-19.0.5.281

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R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

r-abind

1.4-5_gcc-4.9.4
1.4-5_gcc-8.3.0
1.4-5_gcc-9.2.0
1.4-5_intel-19.0.5.281

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Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and higher-dimensional arrays. Also provides functions 'adrop', 'asub', and 'afill' for manipulating, extracting and replacing data in arrays.

r-acepack

1.4.1_gcc-4.9.4
1.4.1_gcc-8.3.0
1.4.1_gcc-9.2.0
1.4.1_intel-19.0.5.281

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ACE and AVAS for Selecting Multiple Regression Transformations.

r-ade4

1.7-13_gcc-8.3.0
1.7-13_gcc-9.2.0

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Analysis of Ecological Data

r-adegenet

2.1.1_gcc-8.3.0
2.1.1_gcc-9.2.0

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Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

r-adegraphics

1.0-15_gcc-8.3.0
1.0-15_gcc-9.2.0

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Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.

r-adephylo

1.1-11_gcc-8.3.0
1.1-11_gcc-9.2.0

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Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.

r-adespatial

0.3-8_gcc-8.3.0
0.3-8_gcc-9.2.0

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Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

r-adgoftest

0.3_gcc-4.9.4
0.3_gcc-8.3.0
0.3_gcc-9.2.0
0.3_intel-19.0.5.281

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Anderson-Darling GoF test with p-value calculation based on Marsaglia's 2004 paper 'Evaluating the Anderson-Darling Distribution'

r-affy

1.62.0_gcc-4.9.4
1.62.0_gcc-8.3.0
1.62.0_gcc-9.2.0
1.62.0_intel-19.0.5.281

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Methods for Affymetrix Oligonucleotide Arrays.

r-affyio

1.54.0_gcc-4.9.4
1.54.0_gcc-8.3.0
1.54.0_gcc-9.2.0
1.54.0_intel-19.0.5.281

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Tools for parsing Affymetrix data files.

randrproto

1.5.0_gcc-9.2.0
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X Resize and Rotate Extension (RandR).

r-annotate

1.62.0_gcc-4.9.4
1.62.0_gcc-8.3.0
1.62.0_gcc-9.2.0
1.62.0_intel-19.0.5.281

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Annotation for microarrays.

r-annotationdbi

1.46.1_gcc-4.9.4
1.46.1_gcc-8.3.0
1.46.1_gcc-9.2.0
1.46.1_intel-19.0.5.281

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Manipulation of SQLite-based annotations in Bioconductor.

r-aod

1.3.1_gcc-4.9.4
1.3.1_gcc-8.3.0
1.3.1_gcc-9.2.0
1.3.1_intel-19.0.5.281

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Provides a set of functions to analyse overdispersed counts or proportions. Most of the methods are already available elsewhere but are scattered in different packages. The proposed functions should be considered as complements to more sophisticated methods such as generalized estimating equations (GEE) or generalized linear mixed effect models (GLMM).

r-ape

5.3_gcc-8.3.0
5.3_gcc-9.2.0

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Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

r-aroma-light

3.16.0_gcc-4.9.4
3.16.0_gcc-8.3.0
3.16.0_gcc-9.2.0
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Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

r-askpass

1.1_gcc-4.9.4
1.1_gcc-8.3.0
1.1_gcc-9.2.0
1.1_intel-19.0.5.281

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Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no 'tcltk' is required. Password entry can be invoked in two different ways: directly from R via the askpass() function, or indirectly as password-entry back-end for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.

r-assertthat

0.2.1_gcc-4.9.4
0.2.1_gcc-8.3.0
0.2.1_gcc-9.2.0
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assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what they've done wrong.

r-backports

1.1.4_gcc-4.9.4
1.1.4_gcc-8.3.0
1.1.4_gcc-9.2.0
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Implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with R (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version.

r-base64

2.0_gcc-4.9.4
2.0_gcc-8.3.0
2.0_gcc-9.2.0
2.0_intel-19.0.5.281

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Compatibility wrapper to replace the orphaned package by Romain Francois. New applications should use the 'openssl' or 'base64enc' package instead.

r-base64enc

0.1-3_gcc-4.9.4
0.1-3_gcc-8.3.0
0.1-3_gcc-9.2.0
0.1-3_intel-19.0.5.281

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This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.

r-beachmat

2.0.0_gcc-4.9.4
2.0.0_gcc-8.3.0
2.0.0_gcc-9.2.0
2.0.0_intel-19.0.5.281

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Compiling Bioconductor to Handle Each Matrix Type.

r-beanplot

1.2_gcc-4.9.4
1.2_gcc-8.3.0
1.2_gcc-9.2.0
1.2_intel-19.0.5.281

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Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot.

r-bh

1.69.0-1_gcc-4.9.4
1.69.0-1_gcc-8.3.0
1.69.0-1_gcc-9.2.0
1.69.0-1_intel-19.0.5.281

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Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN package. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. As of release 1.60.0-2, the following Boost libraries are included: 'algorithm' 'any' 'bimap' 'bind' 'circular_buffer' 'concept' 'config' 'container' 'date'_'time' 'detail' 'dynamic_bitset' 'exception' 'filesystem' 'flyweight' 'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io' 'iostreams' 'iterator' 'math' 'move' 'mpl' 'multiprcecision' 'numeric' 'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit' 'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'.

r-bibtex

0.4.2_gcc-4.9.4
0.4.2_gcc-8.3.0
0.4.2_gcc-9.2.0
0.4.2_intel-19.0.5.281

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bibtex: Bibtex Parser

r-biobase

2.44.0_gcc-4.9.4
2.44.0_gcc-8.3.0
2.44.0_gcc-9.2.0
2.44.0_intel-19.0.5.281

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Biobase: Base functions for Bioconductor.

r-biocgenerics

0.30.0_gcc-4.9.4
0.30.0_gcc-8.3.0
0.30.0_gcc-9.2.0
0.30.0_intel-19.0.5.281

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S4 generic functions used in Bioconductor.

r-biocmanager

1.30.10_gcc-4.9.4
1.30.10_gcc-8.3.0
1.30.10_gcc-9.2.0
1.30.10_intel-19.0.5.281

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BiocManager: Access the Bioconductor Project Package Repository

r-biocparallel

1.18.1_gcc-4.9.4
1.18.1_gcc-8.3.0
1.18.1_gcc-9.2.0
1.18.1_intel-19.0.5.281

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Bioconductor facilities for parallel evaluation.

r-biomart

2.40.5_gcc-4.9.4
2.40.5_gcc-8.3.0
2.40.5_gcc-9.2.0
2.40.5_intel-19.0.5.281

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Interface to BioMart databases (i.e. Ensembl).

r-biomartr

0.9.2_gcc-4.9.4
0.9.2_gcc-8.3.0
0.9.2_gcc-9.2.0
0.9.2_intel-19.0.5.281

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Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', 'ENSEMBLGENOMES', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

r-biostrings

2.52.0_gcc-4.9.4
2.52.0_gcc-8.3.0
2.52.0_gcc-9.2.0
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Efficient manipulation of biological strings.

r-bit

1.1-14_gcc-4.9.4
1.1-14_gcc-8.3.0
1.1-14_gcc-9.2.0
1.1-14_intel-19.0.5.281

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A class for vectors of 1-bit booleans.

r-bit64

0.9-7_gcc-4.9.4
0.9-7_gcc-8.3.0
0.9-7_gcc-9.2.0
0.9-7_intel-19.0.5.281

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Package 'bit64' provides serializable S3 atomic 64bit (signed) integers. These are useful for handling database keys and exact counting in +2^63. WARNING: do not use them as replacement for 32bit integers, integer64 are not supported for subscripting by R-core and they have different semantics when combined with double, e.g. integer64 + double => integer64. Class integer64 can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as 'match' and 'order' support inter active data exploration and manipulation and optionally leverage caching.

r-bitops

1.0-6_gcc-4.9.4
1.0-6_gcc-8.3.0
1.0-6_gcc-9.2.0
1.0-6_intel-19.0.5.281

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Functions for bitwise operations on integer vectors.

r-blob

1.2.0_gcc-4.9.4
1.2.0_gcc-8.3.0
1.2.0_gcc-9.2.0
1.2.0_intel-19.0.5.281

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R's raw vector is useful for storing a single binary object. What if you want to put a vector of them in a data frame? The blob package provides the blob object, a list of raw vectors, suitable for use as a column in data frame.

r-bmp

0.3_gcc-4.9.4
0.3_gcc-8.3.0
0.3_gcc-9.2.0

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Reads Windows BMP format images. Currently limited to 8 bit greyscale images and 24,32 bit (A)RGB images. Pure R implementation without external dependencies.

r-boot

1.3-23_gcc-4.9.4
1.3-23_gcc-8.3.0
1.3-23_gcc-9.2.0
1.3-23_intel-19.0.5.281

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Functions and datasets for bootstrapping from the book 'Bootstrap Methods and Their Application' by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.

r-brew

1.0-6_gcc-4.9.4
1.0-6_gcc-8.3.0
1.0-6_gcc-9.2.0
1.0-6_intel-19.0.5.281

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brew implements a templating framework for mixing text and R code for report generation. brew template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.

r-bsgenome

1.52.0_gcc-4.9.4
1.52.0_gcc-8.3.0
1.52.0_gcc-9.2.0
1.52.0_intel-19.0.5.281

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Software infrastructure for efficient representation of full genomes and their SNPs.

r-bsgenome-hsapiens-ucsc-hg19

1.4.0_gcc-4.9.4
1.4.0_gcc-8.3.0
1.4.0_gcc-9.2.0
1.4.0_intel-19.0.5.281

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Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.

r-bsseq

1.20.0_gcc-4.9.4
1.20.0_gcc-8.3.0
1.20.0_gcc-9.2.0
1.20.0_intel-19.0.5.281

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A collection of tools for analyzing and visualizing bisulfite sequencing data.

r-bumphunter

1.26.0_gcc-4.9.4
1.26.0_gcc-8.3.0
1.26.0_gcc-9.2.0
1.26.0_intel-19.0.5.281

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Bump Hunter.

r-cairo

1.5-10_gcc-4.9.4
1.5-10_gcc-8.3.0
1.5-10_gcc-9.2.0

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R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output

r-callr

3.3.1_gcc-4.9.4
3.3.1_gcc-8.3.0
3.3.1_gcc-9.2.0
3.3.1_intel-19.0.5.281

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It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.

r-car

3.0-3_gcc-4.9.4
3.0-3_gcc-8.3.0
3.0-3_gcc-9.2.0
3.0-3_intel-19.0.5.281

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Functions and Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Second Edition, Sage, 2011.

r-cardata

3.0-2_gcc-4.9.4
3.0-2_gcc-8.3.0
3.0-2_gcc-9.2.0
3.0-2_intel-19.0.5.281

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Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage (forthcoming).

r-caret

6.0-84_gcc-4.9.4
6.0-84_gcc-8.3.0
6.0-84_gcc-9.2.0
6.0-84_intel-19.0.5.281

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Misc functions for training and plotting classification and regression models.

r-catools

1.17.1.2_gcc-4.9.4
1.17.1.2_gcc-8.3.0
1.17.1.2_gcc-9.2.0
1.17.1.2_intel-19.0.5.281

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Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.

r-cellranger

1.1.0_gcc-4.9.4
1.1.0_gcc-8.3.0
1.1.0_gcc-9.2.0
1.1.0_intel-19.0.5.281

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Helper functions to work with spreadsheets and the 'A1:D10' style of cell range specification.

r-checkmate

1.9.4_gcc-4.9.4
1.9.4_gcc-8.3.0
1.9.4_gcc-9.2.0
1.9.4_intel-19.0.5.281

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Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.

r-class

7.3-15_gcc-4.9.4
7.3-15_gcc-8.3.0
7.3-15_gcc-9.2.0
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Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.

r-classint

0.4-1_gcc-8.3.0
0.4-1_gcc-9.2.0

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Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.

r-cli

1.1.0_gcc-4.9.4
1.1.0_gcc-8.3.0
1.1.0_gcc-9.2.0
1.1.0_intel-19.0.5.281

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A suite of tools designed to build attractive command line interfaces ('CLIs'). Includes tools for drawing rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives.

r-clipr

0.7.0_gcc-4.9.4
0.7.0_gcc-8.3.0
0.7.0_gcc-9.2.0
0.7.0_intel-19.0.5.281

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Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.

r-clisymbols

1.2.0_gcc-4.9.4
1.2.0_gcc-8.3.0
1.2.0_gcc-9.2.0
1.2.0_intel-19.0.5.281

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A small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode. Many symbols were taken from the 'figures' 'npm' package (see <https://github.com/sindresorhus/figures>).

r-cluster

2.1.0_gcc-4.9.4
2.1.0_gcc-8.3.0
2.1.0_gcc-9.2.0
2.1.0_intel-19.0.5.281

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Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) 'Finding Groups in Data'.

r-coda

0.19-3_gcc-4.9.4
0.19-3_gcc-8.3.0
0.19-3_gcc-9.2.0
0.19-3_intel-19.0.5.281

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Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.

r-codetools

0.2-16_gcc-4.9.4
0.2-16_gcc-8.3.0
0.2-16_gcc-9.2.0
0.2-16_intel-19.0.5.281

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Code analysis tools for R.

r-codex

1.18.0_gcc-4.9.4
1.18.0_gcc-8.3.0
1.18.0_gcc-9.2.0
1.18.0_intel-19.0.5.281

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A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.

r-colorspace

1.4-1_gcc-4.9.4
1.4-1_gcc-8.3.0
1.4-1_gcc-9.2.0
1.4-1_intel-19.0.5.281

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Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.

r-commonmark

1.7_gcc-4.9.4
1.7_gcc-8.3.0
1.7_gcc-9.2.0
1.7_intel-19.0.5.281

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commonmark: CommonMark and Github Markdown Rendering in R

r-copula

0.999-20_gcc-4.9.4
0.999-20_gcc-8.3.0
0.999-20_gcc-9.2.0
0.999-20_intel-19.0.5.281

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Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.

r-crayon

1.3.4_gcc-4.9.4
1.3.4_gcc-8.3.0
1.3.4_gcc-9.2.0
1.3.4_intel-19.0.5.281

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Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.

r-crosstalk

1.0.0_gcc-4.9.4
1.0.0_gcc-8.3.0
1.0.0_gcc-9.2.0
1.0.0_intel-19.0.5.281

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Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files).

r-cubature

2.0.3_gcc-4.9.4
2.0.3_gcc-8.3.0
2.0.3_gcc-9.2.0
2.0.3_intel-19.0.5.281

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Adaptive multivariate integration over hypercubes

r-curl

4.3_gcc-4.9.4
4.3_gcc-8.3.0
4.3_gcc-9.2.0
4.3_intel-19.0.5.281

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The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), gzip compression, authentication, and other libcurl goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of libcurl is recommended; for a more-user-friendly web client see the 'httr' package which builds on this package with http specific tools and logic.

r-data-table

1.12.2_gcc-4.9.4
1.12.2_gcc-8.3.0
1.12.2_gcc-9.2.0
1.12.2_intel-19.0.5.281

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Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns and a fast file reader (fread). Offers a natural and flexible syntax, for faster development.

r-dbi

1.1.0_gcc-4.9.4
1.1.0_gcc-8.3.0
1.1.0_gcc-9.2.0
1.1.0_intel-19.0.5.281

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A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

r-delayedarray

0.10.0_gcc-4.9.4
0.10.0_gcc-8.3.0
0.10.0_gcc-9.2.0
0.10.0_intel-19.0.5.281

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A unified framework for working transparently with on-disk and in-memory array-like datasets.

r-delayedmatrixstats

1.6.1_gcc-4.9.4
1.6.1_gcc-8.3.0
1.6.1_gcc-9.2.0
1.6.1_intel-19.0.5.281

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Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects.

r-deldir

0.1-23_gcc-8.3.0
0.1-23_gcc-9.2.0

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Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.

r-desc

1.2.0_gcc-4.9.4
1.2.0_gcc-8.3.0
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desc: Manipulate DESCRIPTION Files

r-deseq2

1.24.0_gcc-4.9.4
1.24.0_gcc-8.3.0
1.24.0_gcc-9.2.0
1.24.0_intel-19.0.5.281

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Differential gene expression analysis based on the negative binomial distribution.

r-devtools

2.1.0_gcc-4.9.4
2.1.0_gcc-8.3.0
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Collection of package development tools.

r-diagrammer

1.0.1_gcc-4.9.4
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Create graph diagrams and flowcharts using R.

r-digest

0.6.20_gcc-4.9.4
0.6.20_gcc-8.3.0
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Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the crc32 algorithm is described in ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5, sha-1, sha-256 and aes, this package uses small standalone implementations that were provided by Christophe Devine. For crc32, code from the zlib library is used. For sha-512, an implementation by Aaron D. Gifford is used. For xxhash, the implementation by Yann Collet is used. For murmurhash, an implementation by Shane Day is used. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.

r-dnacopy

1.58.0_gcc-4.9.4
1.58.0_gcc-8.3.0
1.58.0_gcc-9.2.0
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DNA copy number data analysis.

r-dorng

1.7.1_gcc-4.9.4
1.7.1_gcc-8.3.0
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r-downloader

0.4_gcc-4.9.4
0.4_gcc-8.3.0
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Provides a wrapper for the download.file function, making it possible to download files over HTTPS on Windows, Mac OS X, and other Unix-like platforms. The 'RCurl' package provides this functionality (and much more) but can be difficult to install because it must be compiled with external dependencies. This package has no external dependencies, so it is much easier to install.

r-dplyr

0.8.3_gcc-4.9.4
0.8.3_gcc-8.3.0
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A fast, consistent tool for working with data frame like objects, both in memory and out of memory.

r-dss

2.32.0_gcc-4.9.4
2.32.0_gcc-8.3.0
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DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

r-dt

0.8_gcc-4.9.4
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Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.

r-dygraphs

1.1.1.6_gcc-4.9.4
1.1.1.6_gcc-8.3.0
1.1.1.6_gcc-9.2.0
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An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.

r-e1071

1.7-2_gcc-4.9.4
1.7-2_gcc-8.3.0
1.7-2_gcc-9.2.0
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Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, ...

readline

8.0_gcc-4.9.4
8.0_gcc-8.3.0
8.0_gcc-9.2.0
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The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

reditools

1.3_2020-03-20_gcc-9.2.0
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REDItools: python scripts for RNA editing detection by RNA-Seq data.

r-ellipsis

0.2.0.1_gcc-4.9.4
0.2.0.1_gcc-8.3.0
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The ellipsis is a powerful tool for extending functions. Unfortunately this power comes at a cost: misspelled arguments will be silently ignored. The ellipsis package provides a collection of functions to catch problems and alert the user.

renderproto

0.11.1_gcc-4.9.4
0.11.1_gcc-8.3.0
0.11.1_gcc-9.2.0
0.11.1_intel-19.0.5.281

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X Rendering Extension.

repeatmasker

4.0.9_gcc-4.9.4
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RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

r-evaluate

0.14_gcc-4.9.4
0.14_gcc-8.3.0
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Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.

r-exomecopy

1.32.0_gcc-4.9.4
1.32.0_gcc-8.3.0
1.32.0_gcc-9.2.0
1.32.0_intel-19.0.5.281

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Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

r-exomedepth

1.1.15_gcc-4.9.4
1.1.15_gcc-8.3.0
1.1.15_gcc-9.2.0
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Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

r-expm

0.999-4_gcc-8.3.0
0.999-4_gcc-9.2.0

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Computation of the matrix exponential, logarithm, sqrt, and related quantities.

r-fansi

0.4.0_gcc-4.9.4
0.4.0_gcc-8.3.0
0.4.0_gcc-9.2.0
0.4.0_intel-19.0.5.281

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Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.

r-fdb-infiniummethylation-hg18

2.2.0_gcc-4.9.4
2.2.0_gcc-8.3.0
2.2.0_gcc-9.2.0
2.2.0_intel-19.0.5.281

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Compiled HumanMethylation27 and HumanMethylation450 annotations

r-fdb-infiniummethylation-hg19

2.2.0_gcc-4.9.4
2.2.0_gcc-8.3.0
2.2.0_gcc-9.2.0
2.2.0_intel-19.0.5.281

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Compiled HumanMethylation27 and HumanMethylation450 annotations.

r-forcats

0.4.0_gcc-4.9.4
0.4.0_gcc-8.3.0
0.4.0_gcc-9.2.0
0.4.0_intel-19.0.5.281

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Helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, 'anonymising', and manually 'recoding').

r-foreach

1.4.7_gcc-4.9.4
1.4.7_gcc-8.3.0
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Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.

r-foreign

0.8-72_gcc-4.9.4
0.8-72_gcc-8.3.0
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Functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.

r-formatr

1.7_gcc-4.9.4
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Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package.

r-formula

1.2-3_gcc-4.9.4
1.2-3_gcc-8.3.0
1.2-3_gcc-9.2.0
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Infrastructure for extended formulas with multiple parts on the right-hand side and/or multiple responses on the left-hand side.

r-fs

1.3.1_gcc-4.9.4
1.3.1_gcc-8.3.0
1.3.1_gcc-9.2.0
1.3.1_intel-19.0.5.281

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A cross-platform interface to file system operations, built on top of the 'libuv' C library.

r-futile-logger

1.4.3_gcc-4.9.4
1.4.3_gcc-8.3.0
1.4.3_gcc-9.2.0
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Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.

r-futile-options

1.0.1_gcc-4.9.4
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A scoped options management framework

r-future

1.14.0_gcc-4.9.4
1.14.0_gcc-8.3.0
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The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. The simplest way to evaluate an expression in parallel is to use 'x %<-%

Unknown macro: { expression }

' with 'plan(multiprocess)'. This package implements sequential, multicore, multisession, and cluster futures. With these, R expressions can be evaluated on the local machine, in parallel a set of local machines, or distributed on a mix of local and remote machines. Extensions to this package implement additional backends for processing futures via compute cluster schedulers etc. Because of its unified API, there is no need to modify any code in order switch from sequential on the local machine to, say, distributed processing on a remote compute cluster. Another strength of this package is that global variables and functions are automatically identified and exported as needed, making it straightforward to tweak existing code to make use of futures.

r-gdata

2.18.0_gcc-4.9.4
2.18.0_gcc-8.3.0
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Various R programming tools for data manipulation, including: - medical unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects ('bindData', 'cbindX', 'combine', 'interleave'), - character vector operations ('centerText', 'startsWith', 'trim'), - factor manipulation ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll', 'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS-Excel formatted files ('read.xls', 'installXLSXsupport', 'sheetCount', 'xlsFormats'), - generating fixed-width format files ('write.fwf'), - extricating components of date & time objects ('getYear', 'getMonth', 'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'), - operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames ('frameApply', 'wideByFactor'), - value of last evaluated expression ('ans'), and - wrapper for 'sample' that ensures consistent behavior for both scalar and vector arguments ('resample').

r-genefilter

1.66.0_gcc-4.9.4
1.66.0_gcc-8.3.0
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genefilter: methods for filtering genes from high-throughput experiments.

r-geneplotter

1.62.0_gcc-4.9.4
1.62.0_gcc-8.3.0
1.62.0_gcc-9.2.0
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Graphics related functions for Bioconductor.

r-generics

0.0.2_gcc-4.9.4
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In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics.

r-genomeinfodb

1.20.0_gcc-4.9.4
1.20.0_gcc-8.3.0
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Utilities for manipulating chromosome names, including modifying them to follow a particular naming style.

r-genomeinfodbdata

1.2.1_gcc-4.9.4
1.2.1_gcc-8.3.0
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1.2.1_intel-19.0.5.281

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for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.

r-genomicalignments

1.20.1_gcc-4.9.4
1.20.1_gcc-8.3.0
1.20.1_gcc-9.2.0
1.20.1_intel-19.0.5.281

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Representation and manipulation of short genomic alignments.

r-genomicfeatures

1.36.4_gcc-4.9.4
1.36.4_gcc-8.3.0
1.36.4_gcc-9.2.0
1.36.4_intel-19.0.5.281

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Conveniently import and query gene models.

r-genomicranges

1.36.1_gcc-4.9.4
1.36.1_gcc-8.3.0
1.36.1_gcc-9.2.0
1.36.1_intel-19.0.5.281

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Representation and manipulation of genomic intervals.

r-geoquery

2.52.0_gcc-4.9.4
2.52.0_gcc-8.3.0
2.52.0_gcc-9.2.0
2.52.0_intel-19.0.5.281

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Get data from NCBI Gene Expression Omnibus (GEO).

r-ggmap

3.0.0_gcc-4.9.4
3.0.0_gcc-8.3.0
3.0.0_gcc-9.2.0
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A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.

r-ggplot2

3.2.0_gcc-4.9.4
3.2.0_gcc-8.3.0
3.2.0_gcc-9.2.0
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An implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes. See http://ggplot2.org for more information, documentation and examples.

r-ggvis

0.4.4_gcc-4.9.4
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An implementation of an interactive grammar of graphics, taking the best parts of 'ggplot2', combining them with the reactive framework from 'shiny' and web graphics from 'vega'.

r-gh

1.0.1_gcc-4.9.4
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Minimal client to access the 'GitHub' 'API'.

r-git2r

0.26.1_gcc-4.9.4
0.26.1_gcc-8.3.0
0.26.1_gcc-9.2.0
0.26.1_intel-19.0.5.281

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Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.

r-glmnet

2.0-18_gcc-4.9.4
2.0-18_gcc-8.3.0
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Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.

r-globals

0.12.4_gcc-4.9.4
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Identifies global ('unknown' or 'free') objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.

r-glue

1.3.1_gcc-4.9.4
1.3.1_gcc-8.3.0
1.3.1_gcc-9.2.0
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An implementation of interpreted string literals, inspired by Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals <https://docs.julialang.org/en/stable/ manual/strings/#triple-quoted-string-literals>.

r-gmodels

2.18.1_gcc-8.3.0
2.18.1_gcc-9.2.0

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Various R programming tools for model fitting.

r-gmp

0.5-13.5_gcc-4.9.4
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Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), 'arithmetic without limitations' using the C library GMP (GNU Multiple Precision Arithmetic).

r-googlevis

0.6.4_gcc-4.9.4
0.6.4_gcc-8.3.0
0.6.4_gcc-9.2.0
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R interface to Google Charts API, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required and for some charts a Flash player. The data remains local and is not uploaded to Google.

r-gower

0.2.1_gcc-4.9.4
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Compute Gower's distance (or similarity) coefficient between records. Compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.

r-gplots

3.0.1.1_gcc-4.9.4
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Various R Programming Tools for Plotting Data.

r-gridextra

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Provides a number of user-level functions to work with 'grid' graphics, notably to arrange multiple grid-based plots on a page, and draw tables.

r-gsalib

2.1_gcc-4.9.4
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This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.

r-gsl

2.1-6_gcc-4.9.4
2.1-6_gcc-8.3.0
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An R wrapper for some of the functionality of the Gnu Scientific Library.

r-gtable

0.3.0_gcc-4.9.4
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Tools to make it easier to work with 'tables' of 'grobs'.

r-gtools

3.8.1_gcc-4.9.4
3.8.1_gcc-8.3.0
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Functions to assist in R programming.

r-haven

2.1.1_gcc-4.9.4
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Import foreign statistical formats into R via the embedded 'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.

r-hdf5array

1.12.3_gcc-4.9.4
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1.12.3_gcc-9.2.0
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HDF5 backend for DelayedArray objects.

r-hh

3.1-40_gcc-4.9.4
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Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.

r-highr

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Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.

r-hmisc

4.2-0_gcc-4.9.4
4.2-0_gcc-8.3.0
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Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.

r-hms

0.5.0_gcc-4.9.4
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Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.

r-htmltable

1.13.1_gcc-4.9.4
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Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package also contains a few text formatting functions that help outputting text compatible with HTML/'LaTeX'.

r-htmltools

0.3.6_gcc-4.9.4
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Tools for HTML generation and output.

r-htmlwidgets

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A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.

r-httpuv

1.5.1_gcc-4.9.4
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Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)

r-httr

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Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).

r-igraph

1.2.4.1_gcc-4.9.4
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Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

r-illuminahumanmethylation450kanno-ilmn12-hg19

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Manifests and annotation for Illumina's 450k array data.

r-illuminaio

0.26.0_gcc-4.9.4
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Parsing Illumina Microarray Output Files.

r-imager

0.41.2_gcc-4.9.4
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Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.

r-influencer

0.1.0_gcc-4.9.4
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Provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's constraint and effective network size (ENS) metrics, Borgatti's algorithm to identify key players, and Valente's bridging metric. On Unix systems, the betweenness, Key Players, and bridging implementations are parallelized with OpenMP, which may run faster on systems which have OpenMP configured.

r-ini

0.3.1_gcc-4.9.4
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Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.

r-inline

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Functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.

r-ipred

0.9-9_gcc-4.9.4
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Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.

r-iranges

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Foundation of integer range manipulation in Bioconductor.

r-iterators

1.0.12_gcc-4.9.4
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Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.

r-jpeg

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This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.

r-jsonlite

1.6_gcc-4.9.4
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A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of 'RJSONIO', but has been completely rewritten in recent versions. The package offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.

r-kernsmooth

2.23-15_gcc-4.9.4
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Functions for kernel smoothing (and density estimation).

r-knitr

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Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

r-labeling

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Provides a range of axis labeling algorithms.

r-lambda-r

1.2.3_gcc-4.9.4
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A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.

r-later

0.8.0_gcc-4.9.4
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Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied.

r-lattice

0.20-38_gcc-4.9.4
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A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.

r-latticeextra

0.6-28_gcc-4.9.4
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Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.

r-lava

1.6.6_gcc-4.9.4
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Estimation and simulation of latent variable models.

r-lazyeval

0.2.2_gcc-4.9.4
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An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.

r-leaflet

2.0.2_gcc-4.9.4
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Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny apps and R Markdown documents.

r-leaps

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leaps: Regression Subset Selection

r-learnbayes

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LearnBayes contains a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.

r-limma

3.40.6_gcc-4.9.4
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Linear Models for Microarray Data.

r-listenv

0.7.0_gcc-4.9.4
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List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting.

r-lme4

1.1-21_gcc-4.9.4
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Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' 'glue'.

r-lmtest

0.9-37_gcc-4.9.4
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A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.

r-locfit

1.5-9.1_gcc-4.9.4
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Local regression, likelihood and density estimation.

r-loo

2.1.0_gcc-8.3.0
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loo: Efficient Leave-One-Out Cross-Validation and WAIC for BayesianModels

r-lubridate

1.7.4_gcc-4.9.4
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Functions to work with date-times and timespans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and timespan objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.

r-lumi

2.38.0_gcc-4.9.4
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The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

r-magrittr

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Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette.

r-manipulatewidget

0.10.0_gcc-8.3.0
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Like package 'manipulate' does for static graphics, this package helps to easily add controls like sliders, pickers, checkboxes, etc. that can be used to modify the input data or the parameters of an interactive chart created with package 'htmlwidgets'.

r-maps

3.3.0_gcc-4.9.4
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Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').

r-maptools

0.9-5_gcc-4.9.4
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Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.

r-markdown

1.1_gcc-4.9.4
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Provides R bindings to the 'Sundown' 'Markdown' rendering library (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting syntax that can be converted to 'XHTML' or other formats. See http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.

r-mass

7.3-51.4_gcc-4.9.4
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Functions and datasets to support Venables and Ripley, 'Modern Applied Statistics with S' (4th edition, 2002).

r-matrix

1.2-17_gcc-4.9.4
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Classes and methods for dense and sparse matrices and operations on them using 'LAPACK' and 'SuiteSparse'.

r-matrixmodels

0.4-1_gcc-4.9.4
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Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.

r-matrixstats

0.55.0_gcc-4.9.4
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High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().

r-mclust

5.4.5_gcc-4.9.4
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mclust: Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation

r-memoise

1.1.0_gcc-4.9.4
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Cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.

r-methylumi

2.32.0_gcc-4.9.4
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This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An 'intelligent' import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

r-mgcv

1.8-28_gcc-4.9.4
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GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.

r-mime

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Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.

r-minfi

1.30.0_gcc-4.9.4
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Analyze Illumina Infinium DNA methylation arrays.

r-miniui

0.1.1.1_gcc-8.3.0
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Provides UI widget and layout functions for writing Shiny apps that work well on small screens.

r-minqa

1.2.4_gcc-4.9.4
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Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.

r-mitools

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Tools to perform analyses and combine results from multiple-imputation datasets.

r-modelmetrics

1.2.2_gcc-4.9.4
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Collection of metrics for evaluating models written in C++ using 'Rcpp'.

r-multcomp

1.4-10_gcc-4.9.4
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Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book 'Multiple Comparisons Using R' (Bretz, Hothorn, Westfall, 2010, CRC Press).

r-multtest

2.40.0_gcc-4.9.4
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Resampling-based multiple hypothesis testing.

r-munsell

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Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsell's original notation (e.g. '5R 5/10') and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.

r-mvtnorm

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Computes multivariate normal and t probabilities, quantiles, random deviates and densities.

r-ncdf4

1.16.1_gcc-4.9.4
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Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files (either version 4 or 'classic' version 3) can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdf package, which only worked with netcdf version 3 files. For various reasons the names of the functions have had to be changed from the names in the ncdf package. The old ncdf package is still available at the URL given below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4 packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 files.

r-networkd3

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Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.

r-nleqslv

3.3.2_gcc-4.9.4
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nleqslv: Solve Systems of Nonlinear Equations

r-nlme

3.1-141_gcc-4.9.4
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Fit and compare Gaussian linear and nonlinear mixed-effects models.

r-nloptr

1.2.1_gcc-4.9.4
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nloptr is an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See http://ab-initio.mit.edu/wiki/index.php/NLopt _Introduction for more information on the available algorithms. During installation on Unix the NLopt code is downloaded and compiled from the NLopt website.

r-nnet

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Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.

r-nor1mix

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Onedimensional Normal Mixture Models Classes, for, e.g., density estimation or clustering algorithms research and teaching; providing the widely used Marron-Wand densities. Efficient random number generation and graphics; now fitting to data by ML (Maximum Likelihood) or EM estimation.

r-np

0.60-9_gcc-4.9.4
0.60-9_gcc-8.3.0
0.60-9_gcc-9.2.0
0.60-9_intel-19.0.5.281

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This package provides a variety of nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic Research Computing Network (SHARCNET:www.sharcnet.ca).

r-numderiv

2016.8-1.1_gcc-4.9.4
2016.8-1.1_gcc-8.3.0
2016.8-1.1_gcc-9.2.0
2016.8-1.1_intel-19.0.5.281

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Methods for calculating (usually) accurate numerical first and second order derivatives.

r-openssl

1.4.1_gcc-4.9.4
1.4.1_gcc-8.3.0
1.4.1_gcc-9.2.0
1.4.1_intel-19.0.5.281

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Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.

r-openxlsx

4.1.0.1_gcc-4.9.4
4.1.0.1_gcc-8.3.0
4.1.0.1_gcc-9.2.0
4.1.0.1_intel-19.0.5.281

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Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.

r-org-hs-eg-db

3.8.2_gcc-4.9.4
3.8.2_gcc-8.3.0
3.8.2_gcc-9.2.0
3.8.2_intel-19.0.5.281

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Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.

r-packrat

0.5.0_gcc-4.9.4
0.5.0_gcc-8.3.0
0.5.0_gcc-9.2.0
0.5.0_intel-19.0.5.281

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Manage the R packages your project depends on in an isolated, portable, and reproducible way.

r-pbkrtest

0.4-7_gcc-4.9.4
0.4-7_gcc-8.3.0
0.4-7_gcc-9.2.0
0.4-7_intel-19.0.5.281

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Test in mixed effects models. Attention is on mixed effects models as implemented in the 'lme4' package. This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models.

r-pcapp

1.9-73_gcc-4.9.4
1.9-73_gcc-8.3.0
1.9-73_gcc-9.2.0
1.9-73_intel-19.0.5.281

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Provides functions for robust PCA by projection pursuit.

r-permute

0.9-5_gcc-4.9.4
0.9-5_gcc-8.3.0
0.9-5_gcc-9.2.0
0.9-5_intel-19.0.5.281

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A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.

r-philentropy

0.4.0_gcc-4.9.4
0.4.0_gcc-8.3.0
0.4.0_gcc-9.2.0
0.4.0_intel-19.0.5.281

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Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.

r-phylobase

0.8.10_gcc-8.3.0
0.8.10_gcc-9.2.0

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Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

r-pillar

1.4.2_gcc-4.9.4
1.4.2_gcc-8.3.0
1.4.2_gcc-9.2.0
1.4.2_intel-19.0.5.281

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Provides a 'pillar' generic designed for formatting columns of data using the full range of colours provided by modern terminals.

r-pkgbuild

1.0.4_gcc-4.9.4
1.0.4_gcc-8.3.0
1.0.4_gcc-9.2.0
1.0.4_intel-19.0.5.281

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pkgbuild: Find Tools Needed to Build R Packages

r-pkgconfig

2.0.2_gcc-4.9.4
2.0.2_gcc-8.3.0
2.0.2_gcc-9.2.0
2.0.2_intel-19.0.5.281

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Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.

r-pkgload

1.0.2_gcc-4.9.4
1.0.2_gcc-8.3.0
1.0.2_gcc-9.2.0
1.0.2_intel-19.0.5.281

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pkgload: Simulate Package Installation and Attach

r-pkgmaker

0.27_gcc-4.9.4
0.27_gcc-8.3.0
0.27_gcc-9.2.0
0.27_intel-19.0.5.281

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This package provides some low-level utilities to use for package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities. It serves as a base package for packages like NMF, RcppOctave, doRNG, and as an incubator package for other general purposes utilities, that will eventually be packaged separately. It is still under heavy development and changes in the interface(s) are more than likely to happen.

r-plogr

0.2.0_gcc-4.9.4
0.2.0_gcc-8.3.0
0.2.0_gcc-9.2.0
0.2.0_intel-19.0.5.281

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A simple header-only logging library for C+. Add 'LinkingTo: plogr' to 'DESCRIPTION', and '#include <plogr.h>' in your C+ modules to use it.

r-plotrix

3.7-6_gcc-4.9.4
3.7-6_gcc-8.3.0
3.7-6_gcc-9.2.0
3.7-6_intel-19.0.5.281

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Lots of plots, various labeling, axis and color scaling functions.

r-plyr

1.8.4_gcc-4.9.4
1.8.4_gcc-8.3.0
1.8.4_gcc-9.2.0
1.8.4_intel-19.0.5.281

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A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics. The development of 'plyr' has been generously supported by 'Becton Dickinson'.

r-png

0.1-7_gcc-4.9.4
0.1-7_gcc-8.3.0
0.1-7_gcc-9.2.0
0.1-7_intel-19.0.5.281

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This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.

r-praise

1.0.0_gcc-4.9.4
1.0.0_gcc-8.3.0
1.0.0_gcc-9.2.0
1.0.0_intel-19.0.5.281

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Build friendly R packages that praise their users if they have done something good, or they just need it to feel better.

r-preprocesscore

1.46.0_gcc-4.9.4
1.46.0_gcc-8.3.0
1.46.0_gcc-9.2.0
1.46.0_intel-19.0.5.281

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A collection of pre-processing functions.

r-prettyunits

1.0.2_gcc-4.9.4
1.0.2_gcc-8.3.0
1.0.2_gcc-9.2.0
1.0.2_intel-19.0.5.281

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Pretty, human readable formatting of quantities. Time intervals: 1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 1337 -> 1.34 kB.

r-processx

3.4.1_gcc-4.9.4
3.4.1_gcc-8.3.0
3.4.1_gcc-9.2.0
3.4.1_intel-19.0.5.281

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Tools to run system processes in the background

r-prodlim

2018.04.18_gcc-4.9.4
2018.04.18_gcc-8.3.0
2018.04.18_gcc-9.2.0
2018.04.18_intel-19.0.5.281

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Product-Limit Estimation for Censored Event History Analysis. Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.

r-progress

1.2.2_gcc-4.9.4
1.2.2_gcc-8.3.0
1.2.2_gcc-9.2.0
1.2.2_intel-19.0.5.281

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Configurable Progress bars, they may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. The package also provides a 'C++' 'API', that works with or without 'Rcpp'.

r-proj

0.1.0_gcc-4.9.4
0.1.0_gcc-8.3.0
0.1.0_gcc-9.2.0
0.1.0_intel-19.0.5.281

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A wrapper around the generic coordinate transformation software 'PROJ' that transforms geospatial coordinates from one coordinate reference system ('CRS') to another. This includes cartographic projections as well as geodetic transformations. Version 6.0.0 or higher is required. The intention is for this package to be used by user-packages such as 'reproj', and that the older 'PROJ.4' and version 5 pathways be provided by the legacy package. The 'PROJ' library is available from <https://proj.org/>.

r-proj4

1.0-8.1_gcc-4.9.4
1.0-8.1_gcc-8.3.0
1.0-8.1_gcc-9.2.0
1.0-8.1_intel-19.0.5.281

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A simple interface to lat/long projection and datum transformation of the PROJ.4 cartographic projections library. It allows transformation of geographic coordinates from one projection and/or datum to another.

r-promises

1.0.1_gcc-4.9.4
1.0.1_gcc-8.3.0
1.0.1_gcc-9.2.0
1.0.1_intel-19.0.5.281

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Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.

r-ps

1.3.0_gcc-4.9.4
1.3.0_gcc-8.3.0
1.3.0_gcc-9.2.0
1.3.0_intel-19.0.5.281

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Manipulate processes on Windows, Linux and MacOS

r-pscbs

0.65.0_gcc-4.9.4
0.65.0_gcc-8.3.0
0.65.0_gcc-9.2.0
0.65.0_intel-19.0.5.281

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Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

r-pspline

1.0-18_gcc-4.9.4
1.0-18_gcc-8.3.0
1.0-18_gcc-9.2.0
1.0-18_intel-19.0.5.281

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Smoothing splines with penalties on order m derivatives.

r-purrr

0.3.2_gcc-4.9.4
0.3.2_gcc-8.3.0
0.3.2_gcc-9.2.0
0.3.2_intel-19.0.5.281

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A complete and consistent functional programming toolkit for R.

r-quadprog

1.5-7_gcc-4.9.4
1.5-7_gcc-8.3.0
1.5-7_gcc-9.2.0
1.5-7_intel-19.0.5.281

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This package contains routines and documentation for solving quadratic programming problems.

r-quantmod

0.4-15_gcc-4.9.4
0.4-15_gcc-8.3.0
0.4-15_gcc-9.2.0
0.4-15_intel-19.0.5.281

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Specify, build, trade, and analyse quantitative financial trading strategies.

r-quantreg

5.51_gcc-4.9.4
5.51_gcc-8.3.0
5.51_gcc-9.2.0
5.51_intel-19.0.5.281

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Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.

r-r6

2.4.0_gcc-4.9.4
2.4.0_gcc-8.3.0
2.4.0_gcc-9.2.0
2.4.0_intel-19.0.5.281

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The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.

r-randomforest

4.6-14_gcc-4.9.4
4.6-14_gcc-8.3.0
4.6-14_gcc-9.2.0
4.6-14_intel-19.0.5.281

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Classification and regression based on a forest of trees using random inputs.

r-raster

2.9-23_gcc-4.9.4
2.9-23_gcc-8.3.0
2.9-23_gcc-9.2.0
2.9-23_intel-19.0.5.281

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Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.

r-r-cache

0.14.0_gcc-4.9.4
0.14.0_gcc-8.3.0
0.14.0_gcc-9.2.0
0.14.0_intel-19.0.5.281

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Memoization can be used to speed up repetitive and computational expensive function calls. The first time a function that implements memoization is called the results are stored in a cache memory. The next time the function is called with the same set of parameters, the results are momentarily retrieved from the cache avoiding repeating the calculations. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).

r-rcmdcheck

1.3.3_gcc-4.9.4
1.3.3_gcc-8.3.0
1.3.3_gcc-9.2.0
1.3.3_intel-19.0.5.281

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Run 'R CMD check' from 'R' and capture the results of the individual checks. Supports running checks in the background, timeouts, pretty printing and comparing check results.

r-rcolorbrewer

1.1-2_gcc-4.9.4
1.1-2_gcc-8.3.0
1.1-2_gcc-9.2.0
1.1-2_intel-19.0.5.281

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Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org

r-rcpp

1.0.2_gcc-4.9.4
1.0.2_gcc-8.3.0
1.0.2_gcc-9.2.0
1.0.2_intel-19.0.5.281

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The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C+. Many R data types and objects can be mapped back and forth to C+ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation('Rcpp')' for details on these last two.

r-rcpparmadillo

0.9.600.4.0_gcc-4.9.4
0.9.600.4.0_gcc-8.3.0
0.9.600.4.0_gcc-9.2.0
0.9.600.4.0_intel-19.0.5.281

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'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library.

r-rcppeigen

0.3.3.5.0_gcc-4.9.4
0.3.3.5.0_gcc-8.3.0
0.3.3.5.0_gcc-9.2.0
0.3.3.5.0_intel-19.0.5.281

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R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library (currently version 3.2.8). Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.

r-rcurl

1.95-4.12_gcc-4.9.4
1.95-4.12_gcc-8.3.0
1.95-4.12_gcc-9.2.0
1.95-4.12_intel-19.0.5.281

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A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

r-readbitmap

0.1.5_gcc-4.9.4
0.1.5_gcc-8.3.0
0.1.5_gcc-9.2.0

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Identifies and reads Windows BMP, JPEG, PNG, and TIFF format bitmap images. Identification defaults to the use of the magic number embedded in the file rather than the file extension. Reading of JPEG and PNG image depends on libjpg and libpng libraries. See file INSTALL for details if necessary.

r-readr

1.3.1_gcc-4.9.4
1.3.1_gcc-8.3.0
1.3.1_gcc-9.2.0
1.3.1_intel-19.0.5.281

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The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.

r-readxl

1.3.1_gcc-4.9.4
1.3.1_gcc-8.3.0
1.3.1_gcc-9.2.0
1.3.1_intel-19.0.5.281

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Import excel files into R. Supports '.xls' via the embedded 'libxls' C library <https://sourceforge.net/projects/libxls/> and '.xlsx' via the embedded 'RapidXML' C++ library <https://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux without external dependencies.

r-recipes

0.1.6_gcc-4.9.4
0.1.6_gcc-8.3.0
0.1.6_gcc-9.2.0
0.1.6_intel-19.0.5.281

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An extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis 'steps'. Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.

r-registry

0.5-1_gcc-4.9.4
0.5-1_gcc-8.3.0
0.5-1_gcc-9.2.0
0.5-1_intel-19.0.5.281

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Provides a generic infrastructure for creating and using registries.

r-rematch

1.0.1_gcc-4.9.4
1.0.1_gcc-8.3.0
1.0.1_gcc-9.2.0
1.0.1_intel-19.0.5.281

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A small wrapper on 'regexpr' to extract the matches and captured groups from the match of a regular expression to a character vector.

r-remotes

2.1.0_gcc-4.9.4
2.1.0_gcc-8.3.0
2.1.0_gcc-9.2.0
2.1.0_intel-19.0.5.281

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Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.

r-reshape

0.8.8_gcc-4.9.4
0.8.8_gcc-8.3.0
0.8.8_gcc-9.2.0
0.8.8_intel-19.0.5.281

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Flexibly restructure and aggregate data using just two functions: melt and cast.

r-reshape2

1.4.3_gcc-4.9.4
1.4.3_gcc-8.3.0
1.4.3_gcc-9.2.0
1.4.3_intel-19.0.5.281

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Flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).

r-rgdal

1.4-4_gcc-4.9.4
1.4-4_gcc-8.3.0
1.4-4_gcc-9.2.0
1.4-4_intel-19.0.5.281

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Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.6.3) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.

r-rgeos

0.5-1_gcc-4.9.4
0.5-1_gcc-8.3.0
0.5-1_gcc-9.2.0
0.5-1_intel-19.0.5.281

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Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'.

r-rgexf

0.15.3_gcc-4.9.4
0.15.3_gcc-8.3.0
0.15.3_gcc-9.2.0
0.15.3_intel-19.0.5.281

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Create, read and write GEXF (Graph Exchange XML Format) graph files (used in Gephi and others). Using the XML package, it allows the user to easily build/read graph files including attributes, GEXF viz attributes (such as color, size, and position), network dynamics (for both edges and nodes) and edge weighting. Users can build/handle graphs element-by-element or massively through data-frames, visualize the graph on a web browser through 'sigmajs' (a javascript library) and interact with the igraph package.

r-rgl

0.100.26_gcc-8.3.0
0.100.26_gcc-9.2.0

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Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

r-rgooglemaps

1.4.3_gcc-4.9.4
1.4.3_gcc-8.3.0
1.4.3_gcc-9.2.0
1.4.3_intel-19.0.5.281

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This package serves two purposes: Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.

r-rhdf5

2.28.1_gcc-4.9.4
2.28.1_gcc-8.3.0
2.28.1_gcc-9.2.0
2.28.1_intel-19.0.5.281

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R Interface to HDF5.

r-rhdf5lib

1.6.3_gcc-4.9.4
1.6.3_gcc-8.3.0
1.6.3_gcc-9.2.0
1.6.3_intel-19.0.5.281

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hdf5 library as an R package.

r-rhtslib

1.18.1_gcc-4.9.4
1.18.1_gcc-8.3.0
1.18.1_gcc-9.2.0
1.18.1_intel-19.0.5.281

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HTSlib high-throughput sequencing library as an R package.

r-rio

0.5.16_gcc-4.9.4
0.5.16_gcc-8.3.0
0.5.16_gcc-9.2.0
0.5.16_intel-19.0.5.281

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Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate. An additional convenience function, 'convert()', provides a simple method for converting between file types.

r-rjags

4-8_gcc-4.9.4
4-8_gcc-8.3.0
4-8_gcc-9.2.0
4-8_intel-19.0.5.281

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Interface to the JAGS MCMC library. Usage: $ spack load r-rjags

r-rjava

0.9-11_gcc-4.9.4
0.9-11_gcc-8.3.0
0.9-11_gcc-9.2.0
0.9-11_intel-19.0.5.281

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Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.

r-rjson

0.2.20_gcc-4.9.4
0.2.20_gcc-8.3.0
0.2.20_gcc-9.2.0
0.2.20_intel-19.0.5.281

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Converts R object into JSON objects and vice-versa.

r-rlang

0.4.0_gcc-4.9.4
0.4.0_gcc-8.3.0
0.4.0_gcc-9.2.0
0.4.0_intel-19.0.5.281

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A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.

r-rmariadb

1.0.8_gcc-4.9.4
1.0.8_gcc-8.3.0
1.0.8_gcc-9.2.0
1.0.8_intel-19.0.5.281

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Implements a 'DBI'-compliant interface to 'MariaDB' (<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>) databases.

r-rmarkdown

1.14_gcc-8.3.0
1.14_gcc-9.2.0

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Convert R Markdown documents into a variety of formats.

r-r-methodss3

1.7.1_gcc-4.9.4
1.7.1_gcc-8.3.0
1.7.1_gcc-9.2.0
1.7.1_intel-19.0.5.281

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Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.

r-rmpfr

0.7-2_gcc-4.9.4
0.7-2_gcc-8.3.0
0.7-2_gcc-9.2.0
0.7-2_intel-19.0.5.281

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Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ('special') functions. To this end, Rmpfr interfaces to the LGPL'ed MPFR (Multiple Precision Floating-Point Reliable) Library which itself is based on the GMP (GNU Multiple Precision) Library.

r-rmpi

0.6-9_gcc-4.9.4
0.6-9_gcc-8.3.0
0.6-9_gcc-9.2.0
0.6-9_intel-19.0.5.281

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An interface (wrapper) to MPI APIs. It also provides interactive R manager and worker environment.

r-rncl

0.8.4_gcc-8.3.0
0.8.4_gcc-9.2.0

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An interface to the Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'. This functionality is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.

r-rnexml

2.4.5_gcc-8.3.0
2.4.5_gcc-9.2.0

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Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.

r-rngtools

1.4_gcc-4.9.4
1.4_gcc-8.3.0
1.4_gcc-9.2.0
1.4_intel-19.0.5.281

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This package contains a set of functions for working with Random Number Generators (RNGs). In particular, it defines a generic S4 framework for getting/setting the current RNG, or RNG data that are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.

r-roc

1.62.0_gcc-4.9.4
1.62.0_gcc-8.3.0
1.62.0_gcc-9.2.0
1.62.0_intel-19.0.5.281

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Provide utilities for ROC, with microarray focus.

r-rodbc

1.3-15_gcc-4.9.4
1.3-15_gcc-8.3.0
1.3-15_gcc-9.2.0
1.3-15_intel-19.0.5.281

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An ODBC database interface.

r-r-oo

1.23.0_gcc-4.9.4
1.23.0_gcc-8.3.0
1.23.0_gcc-9.2.0
1.23.0_intel-19.0.5.281

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Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.

r-rook

1.1-1_gcc-4.9.4
1.1-1_gcc-8.3.0
1.1-1_gcc-9.2.0
1.1-1_intel-19.0.5.281

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This package contains the Rook specification and convenience software for building and running Rook applications. To get started, be sure and read the 'Rook' help file first.

r-roxygen2

6.1.1_gcc-4.9.4
6.1.1_gcc-8.3.0
6.1.1_gcc-9.2.0
6.1.1_intel-19.0.5.281

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A 'Doxygen'-like in-source documentation system for Rd, collation, and 'NAMESPACE' files.

r-rpart

4.1-15_gcc-4.9.4
4.1-15_gcc-8.3.0
4.1-15_gcc-9.2.0
4.1-15_intel-19.0.5.281

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Recursive partitioning for classification, regression and survival trees.

r-rpostgresql

0.6-2_gcc-4.9.4
0.6-2_gcc-8.3.0
0.6-2_gcc-9.2.0
0.6-2_intel-19.0.5.281

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Database interface and PostgreSQL driver for R This package provides a Database Interface (DBI) compliant driver for R to access PostgreSQL database systems. In order to build and install this package from source, PostgreSQL itself must be present your system to provide PostgreSQL functionality via its libraries and header files. These files are provided as postgresql-devel package under some Linux distributions. On Microsoft Windows system the attached libpq library source will be used. A wiki and issue tracking system for the package are available at Google Code at https://code.google.com/p/rpostgresql/.

r-rprojroot

1.3-2_gcc-4.9.4
1.3-2_gcc-8.3.0
1.3-2_gcc-9.2.0
1.3-2_intel-19.0.5.281

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Robust, reliable and flexible paths to files below a project root. The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.

r-rsamtools

2.2.1_gcc-4.9.4
2.2.1_gcc-8.3.0
2.2.1_gcc-9.2.0
2.2.1_intel-19.0.5.281

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Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import.

r-rsqlite

2.1.2_gcc-4.9.4
2.1.2_gcc-8.3.0
2.1.2_gcc-9.2.0
2.1.2_intel-19.0.5.281

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This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.8.6) is included.

r-rstan

2.19.2_gcc-8.3.0
2.19.2_gcc-9.2.0

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User-facing R functions are provided to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.

r-rstudioapi

0.10_gcc-4.9.4
0.10_gcc-8.3.0
0.10_gcc-9.2.0
0.10_intel-19.0.5.281

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Access the RStudio API (if available) and provide informative error messages when it's not.

r-rtracklayer

1.44.4_gcc-4.9.4
1.44.4_gcc-8.3.0
1.44.4_gcc-9.2.0
1.44.4_intel-19.0.5.281

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R interface to genome annotation files and the UCSC genome browser.

r-r-utils

2.9.0_gcc-4.9.4
2.9.0_gcc-8.3.0
2.9.0_gcc-9.2.0
2.9.0_intel-19.0.5.281

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Utility functions useful when programming and developing R packages.

r-rzmq

0.9.6_gcc-4.9.4
0.9.6_gcc-8.3.0
0.9.6_gcc-9.2.0
0.9.6_intel-19.0.5.281

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Interface to the ZeroMQ lightweight messaging kernel.

r-s4vectors

0.22.1_gcc-4.9.4
0.22.1_gcc-8.3.0
0.22.1_gcc-9.2.0
0.22.1_intel-19.0.5.281

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Foundation of vector-like and list-like containers in Bioconductor.

r-sandwich

2.5-1_gcc-4.9.4
2.5-1_gcc-8.3.0
2.5-1_gcc-9.2.0
2.5-1_intel-19.0.5.281

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Model-robust standard error estimators for cross-sectional, time series, and longitudinal data.

r-scales

1.0.0_gcc-4.9.4
1.0.0_gcc-8.3.0
1.0.0_gcc-9.2.0
1.0.0_intel-19.0.5.281

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Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.

r-scrime

1.3.5_gcc-4.9.4
1.3.5_gcc-8.3.0
1.3.5_gcc-9.2.0
1.3.5_intel-19.0.5.281

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scrime: Analysis of High-Dimensional Categorical Data Such as SNP Data

r-segmented

1.0-0_gcc-8.3.0
1.0-0_gcc-9.2.0

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Given a regression model, segmented 'updates' the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.

rsem

1.3.1_gcc-9.2.0
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RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

r-seqinr

3.4-5_gcc-8.3.0
3.4-5_gcc-9.2.0

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Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Includes also utilities for sequence data management under the ACNUC system.

r-sessioninfo

1.1.1_gcc-4.9.4
1.1.1_gcc-8.3.0
1.1.1_gcc-9.2.0
1.1.1_intel-19.0.5.281

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Query and print information about the current R session. It is similar to 'utils::sessionInfo()', but includes more information about packages, and where they were installed from.

r-sf

0.7-7_gcc-8.3.0
0.7-7_gcc-9.2.0

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Support for simple features, a standardized way to encode spatial vector data. Binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to Proj.4 for projection conversions and datum transformations.

r-shiny

1.3.2_gcc-4.9.4
1.3.2_gcc-8.3.0
1.3.2_gcc-9.2.0
1.3.2_intel-19.0.5.281

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Makes it incredibly easy to build interactive web applications with R. Automatic 'reactive' binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.

r-siggenes

1.58.0_gcc-4.9.4
1.58.0_gcc-8.3.0
1.58.0_gcc-9.2.0
1.58.0_intel-19.0.5.281

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Multiple Testing using SAM and Efron's Empirical Bayes Approaches.

r-snow

0.4-3_gcc-4.9.4
0.4-3_gcc-8.3.0
0.4-3_gcc-9.2.0
0.4-3_intel-19.0.5.281

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Support for simple parallel computing in R.

r-sourcetools

0.1.7_gcc-4.9.4
0.1.7_gcc-8.3.0
0.1.7_gcc-9.2.0
0.1.7_intel-19.0.5.281

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Tools for Reading, Tokenizing and Parsing R Code.

r-sp

1.3-1_gcc-4.9.4
1.3-1_gcc-8.3.0
1.3-1_gcc-9.2.0
1.3-1_intel-19.0.5.281

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Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.

r-sparsem

1.77_gcc-4.9.4
1.77_gcc-8.3.0
1.77_gcc-9.2.0
1.77_intel-19.0.5.281

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Some basic linear algebra functionality for sparse matrices is provided: including Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.

r-spdata

0.3.0_gcc-8.3.0
0.3.0_gcc-9.2.0

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spData: Datasets for Spatial Analysis

r-spdep

1.1-2_gcc-8.3.0
1.1-2_gcc-9.2.0

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A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic, Empirical Bayes estimates and AssunasReis Index, Getis/Ord G and multicoloured join count statistics, local Moran's I and Getis/Ord G, saddlepoint approximations and exact tests for global and local Moran's I; and functions for estimating spatial simultaneous autoregressive (SAR) lag and error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression models, semi-parametric and Moran eigenvector spatial filtering, GM SAR error models, and generalized spatial two stage least squares models.

r-squarem

2017.10-1_gcc-4.9.4
2017.10-1_gcc-8.3.0
2017.10-1_gcc-9.2.0
2017.10-1_intel-19.0.5.281

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Algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent acceleration scheme. A tutorial style introduction to this package is available in a vignette on the CRAN download page or, when the package is loaded in an R session, with vignette('SQUAREM').

r-stabledist

0.7-1_gcc-4.9.4
0.7-1_gcc-8.3.0
0.7-1_gcc-9.2.0
0.7-1_intel-19.0.5.281

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Density, Probability and Quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan.

r-stanheaders

2.18.1-10_gcc-8.3.0
2.18.1-10_gcc-9.2.0

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The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.

r-stringi

1.4.3_gcc-4.9.4
1.4.3_gcc-8.3.0
1.4.3_gcc-9.2.0
1.4.3_intel-19.0.5.281

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Allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g., with ICU Java-like regular expressions or the Unicode Collation Algorithm), random string generation, case mapping, string transliteration, concatenation, Unicode normalization, date-time formatting and parsing, etc.

r-stringr

1.4.0_gcc-4.9.4
1.4.0_gcc-8.3.0
1.4.0_gcc-9.2.0
1.4.0_intel-19.0.5.281

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A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with 'NA''s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.

r-summarizedexperiment

1.14.1_gcc-4.9.4
1.14.1_gcc-8.3.0
1.14.1_gcc-9.2.0
1.14.1_intel-19.0.5.281

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SummarizedExperiment container.

r-suppdists

1.1-9.5_gcc-4.9.4
1.1-9.5_gcc-8.3.0
1.1-9.5_gcc-9.2.0
1.1-9.5_intel-19.0.5.281

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Ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions.

r-survey

3.36_gcc-4.9.4
3.36_gcc-8.3.0
3.36_gcc-9.2.0
3.36_intel-19.0.5.281

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Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.

r-survival

2.44-1.1_gcc-4.9.4
2.44-1.1_gcc-8.3.0
2.44-1.1_gcc-9.2.0
2.44-1.1_intel-19.0.5.281

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Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

r-sys

3.2_gcc-4.9.4
3.2_gcc-8.3.0
3.2_gcc-9.2.0
3.2_intel-19.0.5.281

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Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales.

r-tarifx

1.0.6.1_gcc-4.9.4
1.0.6.1_gcc-8.3.0
1.0.6.1_gcc-9.2.0
1.0.6.1_intel-19.0.5.281

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A collection of various utility and convenience functions.

r-testthat

2.2.1_gcc-4.9.4
2.2.1_gcc-8.3.0
2.2.1_gcc-9.2.0
2.2.1_intel-19.0.5.281

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A unit testing system designed to be fun, flexible and easy to set up.

r-th-data

1.0-10_gcc-4.9.4
1.0-10_gcc-8.3.0
1.0-10_gcc-9.2.0
1.0-10_intel-19.0.5.281

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Contains data sets used in other packages Torsten Hothorn maintains.

r-threejs

0.3.1_gcc-4.9.4
0.3.1_gcc-8.3.0
0.3.1_gcc-9.2.0
0.3.1_intel-19.0.5.281

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Create interactive 3D scatter plots, network plots, and globes using the 'three.js' visualization library ('http://threejs.org').

r-tibble

2.1.3_gcc-4.9.4
2.1.3_gcc-8.3.0
2.1.3_gcc-9.2.0
2.1.3_intel-19.0.5.281

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Provides a 'tbl_df' class that offers better checking and printing capabilities than traditional data frames.

r-tidyr

0.8.3_gcc-4.9.4
0.8.3_gcc-8.3.0
0.8.3_gcc-9.2.0
0.8.3_intel-19.0.5.281

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An evolution of 'reshape2'. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with 'dplyr' data pipelines.

r-tidyselect

0.2.5_gcc-4.9.4
0.2.5_gcc-8.3.0
0.2.5_gcc-9.2.0
0.2.5_intel-19.0.5.281

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A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.

r-tiff

0.1-5_gcc-4.9.4
0.1-5_gcc-8.3.0
0.1-5_gcc-9.2.0

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This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.

r-timedate

3043.102_gcc-4.9.4
3043.102_gcc-8.3.0
3043.102_gcc-9.2.0
3043.102_intel-19.0.5.281

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Environment for teaching 'Financial Engineering and Computational Finance'. Managing chronological and calendar objects.

r-tinytex

0.15_gcc-8.3.0
0.15_gcc-9.2.0

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Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.

r-ttr

0.23-4_gcc-4.9.4
0.23-4_gcc-8.3.0
0.23-4_gcc-9.2.0
0.23-4_intel-19.0.5.281

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Functions and data to construct technical trading rules with R.

r-txdb-hsapiens-ucsc-hg18-knowngene

3.2.2_gcc-4.9.4
3.2.2_gcc-8.3.0
3.2.2_gcc-9.2.0
3.2.2_intel-19.0.5.281

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Exposes an annotation databases generated from UCSC by exposing these as TxDb objects

r-txdb-hsapiens-ucsc-hg19-knowngene

3.2.2_gcc-4.9.4
3.2.2_gcc-8.3.0
3.2.2_gcc-9.2.0
3.2.2_intel-19.0.5.281

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Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-units

0.6-3_gcc-8.3.0
0.6-3_gcc-9.2.0

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Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion.

r-usethis

1.5.1_gcc-4.9.4
1.5.1_gcc-8.3.0
1.5.1_gcc-9.2.0
1.5.1_intel-19.0.5.281

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Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

r-utf8

1.1.4_gcc-4.9.4
1.1.4_gcc-8.3.0
1.1.4_gcc-9.2.0
1.1.4_intel-19.0.5.281

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Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.

r-uuid

0.1-2_gcc-8.3.0
0.1-2_gcc-9.2.0

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Tools for generating and handling of UUIDs (Universally Unique Identifiers).

r-vcd

1.4-4_gcc-4.9.4
1.4-4_gcc-8.3.0
1.4-4_gcc-9.2.0
1.4-4_intel-19.0.5.281

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Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was package was originally inspired by the book 'Visualizing Categorical Data' by Michael Friendly and is now the main support package for a new book, 'Discrete Data Analysis with R' by Michael Friendly and David Meyer (2015).

r-vctrs

0.2.0_gcc-4.9.4
0.2.0_gcc-8.3.0
0.2.0_gcc-9.2.0
0.2.0_intel-19.0.5.281

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Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analyzing function interfaces.

r-vegan

2.5-5_gcc-8.3.0
2.5-5_gcc-9.2.0

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Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

r-vgam

1.1-1_gcc-4.9.4
1.1-1_gcc-8.3.0
1.1-1_gcc-9.2.0
1.1-1_intel-19.0.5.281

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An implementation of about 6 major classes of statistical regression models.

r-viridis

0.5.1_gcc-4.9.4
0.5.1_gcc-8.3.0
0.5.1_gcc-9.2.0
0.5.1_intel-19.0.5.281

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viridis: Default Color Maps from 'matplotlib'

r-viridislite

0.3.0_gcc-4.9.4
0.3.0_gcc-8.3.0
0.3.0_gcc-9.2.0
0.3.0_intel-19.0.5.281

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viridisLite: Default Color Maps from 'matplotlib' (Lite Version)

r-visnetwork

2.0.7_gcc-4.9.4
2.0.7_gcc-8.3.0
2.0.7_gcc-9.2.0
2.0.7_intel-19.0.5.281

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Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.

r-watermelon

1.30.0_gcc-4.9.4
1.30.0_gcc-8.3.0
1.30.0_gcc-9.2.0
1.30.0_intel-19.0.5.281

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Illumina 450 methylation array normalization and metrics.

r-webshot

0.5.1_gcc-8.3.0
0.5.1_gcc-9.2.0

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webshot: Take Screenshots of Web Pages

r-whisker

0.3-2_gcc-4.9.4
0.3-2_gcc-8.3.0
0.3-2_gcc-9.2.0
0.3-2_intel-19.0.5.281

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logicless templating, reuse templates in many programming languages including R

r-withr

2.1.2_gcc-4.9.4
2.1.2_gcc-8.3.0
2.1.2_gcc-9.2.0
2.1.2_intel-19.0.5.281

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A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.

r-xfun

0.8_gcc-4.9.4
0.8_gcc-8.3.0
0.8_gcc-9.2.0
0.8_intel-19.0.5.281

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Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.

r-xlconnect

0.2-15_gcc-4.9.4
0.2-15_gcc-8.3.0
0.2-15_gcc-9.2.0
0.2-15_intel-19.0.5.281

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Provides comprehensive functionality to read, write and format Excel data.

r-xlconnectjars

0.2-15_gcc-4.9.4
0.2-15_gcc-8.3.0
0.2-15_gcc-9.2.0
0.2-15_intel-19.0.5.281

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Provides external JAR dependencies for the XLConnect package.

r-xlsx

0.6.1_gcc-4.9.4
0.6.1_gcc-8.3.0
0.6.1_gcc-9.2.0
0.6.1_intel-19.0.5.281

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Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.

r-xlsxjars

0.6.1_gcc-4.9.4
0.6.1_gcc-8.3.0
0.6.1_gcc-9.2.0
0.6.1_intel-19.0.5.281

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The xlsxjars package collects all the external jars required for the xlxs package. This release corresponds to POI 3.10.1.

r-xml

3.98-1.20_gcc-4.9.4
3.98-1.20_gcc-8.3.0
3.98-1.20_gcc-9.2.0
3.98-1.20_intel-19.0.5.281

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Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' 'interpreter'.

r-xml2

1.2.2_gcc-4.9.4
1.2.2_gcc-8.3.0
1.2.2_gcc-9.2.0
1.2.2_intel-19.0.5.281

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Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.

r-xopen

1.0.0_gcc-4.9.4
1.0.0_gcc-8.3.0
1.0.0_gcc-9.2.0
1.0.0_intel-19.0.5.281

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Cross platform solution to open files, directories or 'URLs' with their associated programs.

r-xtable

1.8-4_gcc-4.9.4
1.8-4_gcc-8.3.0
1.8-4_gcc-9.2.0
1.8-4_intel-19.0.5.281

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Coerce data to LaTeX and HTML tables.

r-xts

0.11-2_gcc-4.9.4
0.11-2_gcc-8.3.0
0.11-2_gcc-9.2.0
0.11-2_intel-19.0.5.281

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Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.

r-xvector

0.24.0_gcc-4.9.4
0.24.0_gcc-8.3.0
0.24.0_gcc-9.2.0
0.24.0_intel-19.0.5.281

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Foundation of external vector representation and manipulation in Bioconductor.

r-yaml

2.2.0_gcc-4.9.4
2.2.0_gcc-8.3.0
2.2.0_gcc-9.2.0
2.2.0_intel-19.0.5.281

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This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.

r-zeallot

0.1.0_gcc-4.9.4
0.1.0_gcc-8.3.0
0.1.0_gcc-9.2.0
0.1.0_intel-19.0.5.281

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Provides a %<-% operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.

r-zip

2.0.3_gcc-4.9.4
2.0.3_gcc-8.3.0
2.0.3_gcc-9.2.0
2.0.3_intel-19.0.5.281

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Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.

r-zlibbioc

1.30.0_gcc-4.9.4
1.30.0_gcc-8.3.0
1.30.0_gcc-9.2.0
1.30.0_intel-19.0.5.281

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An R packaged zlib-1.2.5.

r-zoo

1.8-6_gcc-4.9.4
1.8-6_gcc-8.3.0
1.8-6_gcc-9.2.0
1.8-6_intel-19.0.5.281

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An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.

samtools

1.10_gcc-4.9.4
1.10_gcc-8.3.0
1.10_gcc-9.2.0
1.10_intel-19.0.5.281

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SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format

scotch

6.0.8_gcc-9.2.0
6.0.8_intel-19.0.5.281

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Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering.

sdl2

2.0.5_gcc-4.9.4
2.0.5_gcc-8.3.0
2.0.5_gcc-9.2.0

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Simple DirectMedia Layer is a cross-platform development library designed to provide low level access to audio, keyboard, mouse, joystick, and graphics hardware via OpenGL and Direct3D.

shared-mime-info

1.9_gcc-8.3.0
1.9_gcc-9.2.0

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Database of common MIME types.

snap-korf

2013-11-29_gcc-4.9.4
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SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.