This material is linked to a face-to-face training. It is not intended to be followed via e-learning only because not all info is here.

Material

• • Slides for this course
  • Data set for this course
  • Bash script to perform Galaxy pipeline on command line: it implies that you have all tools installed . Note that you will have to adjust paths so that they work on your computer and with the versions of the tools that you have installed.

DESeq2

• • Tutorial for this course
  • R markdown for this course

• • Basic R script for this course

• • Script to start day 2

EdgeR

• • Tutorial for EdgeR
  • R markdown for EdgeR
  • Basic R script for EdgeR

Limma Voom

• • Basic R script for using a blocking factor in Limma Voom (works also for unbalanced designs)

Tools for counting

All counting tools will be used on the Belgian Galaxy server.

• • HTSeq count

• • FeatureCounts

• • Kallisto

• • Salmon

• • STAR

Tools for Differential Gene Expression

All tools are Bioconductor packages that are used in RStudio. Scripts can be downloaded above.

• • DESeq2

• • EdgeR

Tools for Batch correction

All tools are Bioconductor packages that are used in RStudio.

• • ComBat-seq

• • SVA

Tools for Differential Transcript Usage

All tools are Bioconductor packages that are used in RStudio.

• • DEXSeq

• • DRIMSeq