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Day 1: Wed, June 8th

 

Location

Time

Title - Click to listen to recording

Instructor

Slides/Lab Instructions

1st Floor PBDB (outside of rm 1459)8:00-8:30Check In – Coffee and Tea provided 

 

1459 PBDB8:30-8:45Course OverviewTom Bair, PhDWelcome_2016.pdf
1459 PBDB8:45-9:45

Enabling Data Driven Research at UW Medicine

Sean Mooney, PhD

Iowa_crio_6816.1.pdf
1st Floor Lobby PBDB9:45-10:00Break  
1459 PBDB10:00-11:00

Characterization of retinal ganglion cell subtypes by single cell RNA-seq

Jeff Trimarchi, PhD

Slides part 1.pdf

Slides part 2.pdf

1459 PBDB11:00-12:00

Probabilistic Identification of Impactful and Disease Associated Genetic Variants

Sean Mooney, PhD

Iowa_6816.1.pdf

1st Floor PBDB (outside of Rm. 1459)12:00-1:15Lunch (Taco Bar)  
Hardin Library Information Commons East1:30 - 5:00 PM

Basic R Hands-on Training:

Learn how to get starting with R using the Rstudio interface. This course will assume no starting knowledge and will get you to a point where you will feel comfortable with starting to work with data in R. It is a steep learning curve but worth it as R is one of the best data analysis tools and is extensively used in the bioinformatics field

Rama Sompallae, PhD

R basic slides

 

 

Day 2: Thur, June 9th

Location

Time

Title - Click to listen to recording

Instructor

Slides/Lab Instructions

1459 PBDB9:00-10:00

Learning Gene Networks from Single Cell RNA-Seq

Andrew McDavid

gene_networks_iowa.pdf
1st Floor Lobby PBDB10:00-10:15Break  
1459 PBDB10:15-11:15Exome sequencing case talkDiana Kolbe, PhDkolbe-exomes-20160609.pdf
1459 PBDB11:15-12:00

Examination of sequencing data in three Israeli families with Keratoconus

Wesley Goar, PhD candidateBSC_WG.pdf
1st Floor PBDB (outside of Rm. 1459)12:00-1:00Lunch (The Wedge Pizza)  
Hardin Library Information Commons East1:15 - 5:00 PM

Kalisto-Sleuth Hands-on training:


Learn how to quickly get an RNA-seq data from raw fastq to statistically relevant results that are easy to visualize and understand. This course will assume some knowledge of R such as the basic R class from the previous day.

Michael Chimenti, PhDkallisto-sleuth-intro-talk.pdf, kallisto data files, sleuth_exercises.pdf

Day 3: Fri, June 10th

Location

Time

Title - Click to listen to recording

Instructor

Slides/Lab Instructions

283 EMRB (Seebohm)9:00-10:00

Predicting Cell Phenotype from Single Cell RNA-Seq

Andrew McDavid

single_cell_classifiers.pdf
283 EMRB (Seebohm)10:00-10:15Break  
283 EMRB (Seebohm)10:15-11:15

RNA Sequencing of Human Donor Eyes: From Whole Tissues to Single Cells

Scott Whitmore, PhD 
283 EMRB (Seebohm)11:15-12:00Metagenomics

Michael Chimenti, PhD and Kate O'Brien

 
283 EMRB (Seebohm)12:00-1:00Lunch (Jimmy John's Sandwiches)  
Hardin Library Information Commons East1:00 - 5:00 PM

RStudio Hands-on training – intermediate:

As demonstrated in the previous sessions, R is a powerful statistical programming language for manipulating, analyzing, and graphing data.  In this class, you will learn more about the presentation of data and analysis results in R.   We will begin with an introduction to basic presentation tools and work our way up to the development of interactive web applications using the RStudio Shiny package.  With Shiny, you will be able to create web applications using only the R programming language.  No HTML, CSS, or JavaScript knowledge required.  Come prepared to do some coding and experimentation.

Brian J. Smith, PhD

RShiny.pdf

RShiny.R

RGraphics.R

West.rdata

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