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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "GExPipe" in publications use:'
type: software
license: MIT
title: 'GExPipe: GExPipe: Gene Expression Pipeline Shiny Application'
version: 0.99.43
doi: 10.32614/CRAN.package.GExPipe
abstract: '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.'
authors:
- family-names: Rafique
  given-names: Safa
  email: safa.sandhu@gmail.com
  orcid: https://orcid.org/0000-0003-2646-8106
- family-names: Ashraf
  given-names: Naeem Mahmood
  email: naeem.sbb@pu.edu.pk
- family-names: Sabar
  given-names: Prof. Dr. Muhammad Farooq
  email: farooq.sbb@pu.edu.pk
repository: https://bioc.r-universe.dev
repository-code: https://github.com/safarafique/GExPipe
commit: ffd15467eec4f74451eaf9d66a90b39897a765d8
url: https://github.com/safarafique/GExPipe
date-released: '2026-07-22'
contact:
- family-names: Rafique
  given-names: Safa
  email: safa.sandhu@gmail.com
  orcid: https://orcid.org/0000-0003-2646-8106