GExPipe

GExPipe: Gene Expression Pipeline Shiny Application

Bioconductor version: 3.24 · Package version: 0.99.51

Shiny application (GExPipe) for high-throughput genomic analysis of bulk RNA-seq and microarray data (e.g. from GEO). Integrates with Bioconductor (GEOquery, Biobase, limma, DESeq2, edgeR, clusterProfiler) for a single workflow: download, QC, normalization, batch correction, differential expression, WGCNA, pathway enrichment, PPI, and machine learning. Uses common data structures (ExpressionSet, DGEList) for interoperability. For a full dependency tree (including STRINGdb + PPI helpers), use BiocManager::install("GExPipe", dependencies = TRUE). STRING data are downloaded on first PPI use (internet required); they cannot be bundled in the package. Microarray CEL normalization uses affy and/or oligo when supplementary CEL files are available.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GExPipe")