GExPipe
Bioc removedGExPipe: Gene Expression Pipeline Shiny Application
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Description
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.
None published for Bioconductor
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People
- Safa Rafique author maintainer
- Naeem Mahmood Ashraf author
- Prof. Dr. Muhammad Farooq Sabar author
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