tximport to edgeR
Build an edgeR DGEList from gene-level tximport output, checking gene IDs, sample alignment, and library sizes.
Count-aware edgeR import and QC, differential-expression reminders, ranked enrichment, and sample-level gene-set scores.
Bulk RNA QC and normalization
Check sample quality, filter low-expression genes, estimate library-composition normalization, and create logCPM values.
Differential expression with edgeR
Provide an edgeR quasi-likelihood reminder for a biological contrast from a filtered, normalized DGEList.
Ranked gene-set enrichment
Run GO Biological Process and optional KEGG GSEA from a complete ranked gene-level statistic table.
Sample-level signature scoring with singscore
Score a directional gene signature in each sample using within-sample ranks.
Sample-level gene-set activity with GSVA
Transform a gene-by-sample expression matrix into gene-set-by-sample activity scores with GSVA.