Bulk RNA-seq Differential Expression & Enrichment Analysis
A Snakemake pipeline that performs differential expression analysis on Salmon-quantified Bulk RNA-seq data using edgeR (TMM/quasi-likelihood), followed by downstream functional enrichment analyses including GO over-representation, GSEA, Reactome pathway analysis, and Hallmark gene-set scoring. Outputs include DEG Excel tables, volcano plots, and enrichment plots.
VERSION 1.0.0
AUTHOR Yeongjun-git
INPUT tx2gene.tsvmetadata.csvSalmon quant.sf filesHallmark gene-set GMT (optional)
OUTPUT DEG Excel tablesTPM expression matrixTMM normalized count matrixVolcano & enrichment plots
FILES
Select a file from the tree to view its contents.