{ "_id": "6ae1420195ca2370cc8caeeb", "Package": "GExPipe", "Title": "GExPipe: Gene Expression Pipeline Shiny Application", "Version": "0.99.117", "Authors@R": "c(\nperson(\ngiven = \"Safa\",\nfamily = \"Rafique\",\nemail = \"safa.sandhu@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-2646-8106\")\n),\nperson(\ngiven = \"Naeem Mahmood\",\nfamily = \"Ashraf\",\nemail = \"naeem.sbb@pu.edu.pk\",\nrole = \"aut\"\n),\nperson(\ngiven = \"Prof. Dr. Muhammad Farooq\",\nfamily = \"Sabar\",\nemail = \"farooq.sbb@pu.edu.pk\",\nrole = \"aut\"\n)\n)", "Description": "Shiny application (GExPipe) for high-throughput genomic\nanalysis of bulk RNA-seq and microarray data (e.g. from GEO).\nFour analysis types: RNA-seq only, microarray only, Merged\n(Both) (per-dataset normalize then one joint batch and limma\nDE), and Parallel DE then merge (separate pipelines through DE,\nthen RNA-seq intersect microarray). Each RNA-seq and microarray\nbox accepts one or more GSE IDs in the same run. Integrates\nwith Bioconductor (GEOquery, Biobase, limma, DESeq2, edgeR,\nclusterProfiler) for download, QC, normalization, batch\ncorrection, differential expression, WGCNA, pathway enrichment,\nPPI, and machine learning. Uses common data structures\n(ExpressionSet, DGEList) for interoperability. For a full\ndependency tree (including STRINGdb + PPI helpers), use\nBiocManager::install(\"GExPipe\", dependencies = TRUE). STRING\ndata are downloaded on first PPI use (internet required); they\ncannot be bundled in the package. Microarray CEL normalization\nuses affy and/or oligo when supplementary CEL files are\navailable.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "biocViews": "Software, ShinyApps, GeneExpression, RNASeq, Microarray,\nDifferentialExpression, Normalization, Pathways, Network,\nNetworkEnrichment, Visualization", "URL": "https://github.com/safarafique/GExPipe", "BugReports": "https://github.com/safarafique/GExPipe/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "SystemRequirements": "GNU make", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-27 22:25:41 UTC", "RemoteUrl": "https://github.com/bioc/GExPipe", "RemoteRef": "HEAD", "RemoteSha": "ddd5cafbf45b46916577d9a5154d103c4b57c411", 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