transcriptutorial

This is a tutorial to guide the analysis of RNAseq datasets using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL.

For details instructions to setup the transcriptutorial (data, software, R packages, etc), visit INSTALL.md.

This tutorial is split into several sections, from normalisation to causal network analysis. Once set up, you may run each step sequentially. The corresponding R markdown scripts for each of those sections can be found in the scripts subfolder.

https://github.com/saezlab/transcriptutorial/blob/master/scripts/01_normalisation.md

https://github.com/saezlab/transcriptutorial/blob/master/scripts/02_differential_analysis.md

https://github.com/saezlab/transcriptutorial/blob/master/scripts/03_Pathway_activity_with_Progeny.md

https://github.com/saezlab/transcriptutorial/blob/master/scripts/04_TranscriptionFactor_activity_with_Dorothea.md

https://github.com/saezlab/transcriptutorial/blob/master/scripts/05_network_reconstruction_with_CARNIVAL.md

https://github.com/saezlab/transcriptutorial/blob/master/scripts/06_analysis_CARNIVAL_results.md

For any question/suggestions, we encourage you to use the issue submission system :)

Have fun !!