bulk rnasEQ ANALYSIS

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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

    • 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

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.

Tools for Batch correction

All tools are Bioconductor packages that are used in RStudio.

Tools for Differential Transcript Usage

All tools are Bioconductor packages that are used in RStudio.

Contributors: Janick Mathys, Charlotte Soneson, Rekin’s Janky, Stephane Plaisance, Paul De Geest, Kobe Lavaerts

Created by Janick Mathys