RNAseqWizard
Interactive Shiny app for bulk RNA-seq QC, differential expression, and pathway analysis
RNAseqWizard is a Shiny app for end-to-end bulk RNA-seq analysis. It takes raw count matrices and a sample metadata file and walks you through a complete pipeline: library-size QC, density-based filtering, and PCA for quality control; TMM normalization and edgeR GLM-based differential expression (two-group, all pairwise, or omnibus); volcano plots, MA plots, and expression heatmaps for visualization; CPM boxplots with pairwise statistics for genes of interest; and pathway analysis via GSEA (fgsea), GSVA, or o ver-representation analysis (ORA) against MSigDB collections or custom GMT files. Results can be exported as publication-ready PDFs and a compiled R Markdown report.
- Code: github.com/nourabdelfattah/RNAseqWizard
- Run it locally:
shiny::runGitHub("RNAseqWizard", "nourabdelfattah")