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
EdgeR
- Tutorial for EdgeR
- R markdown for EdgeR
- Basic R script for EdgeR
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.
