zhefrench/toulouse

Toulouse Project - RNA-SEQ

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Compute differential gene expression, find patterns of expression and do some gene ontology and gsea analysis.

Execute scripts in src directory. It called files using relative paths.

1. dge-6.R - Differential gene expression based on count matrix. Create gene-selection and gene-ratio which are the same things, just the format differs.

2. pattern-selection-1.R

3. geneOntologyEnrichment.R

4. merge.counts.R

5. ssGSEA.R (I'm not using it finally)

6. fGSEA.R

7. heatmap-fGSEA.R write table for specific terms with good p-values to use for an heatmap with Morpheus online tool.

8. heatmap-customGenes.R

9. cluster.ontology.R

10. heatmap-customGenes.R

Print matrice in file in order to draw heatmap.