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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 "OncoSeq" in publications use:'
type: software
license: GPL-3.0-only
title: 'OncoSeq: End-to-End Analysis of Cancer Transcriptomes and Genomes'
version: 0.99.1
doi: 10.32614/CRAN.package.OncoSeq
abstract: OncoSeq provides a unified, end-to-end workflow for cancer transcriptomic
  and genomic data analysis. A single container class couples bulk RNA-sequencing
  counts with somatic mutation calls, gene-level copy-number alterations and clinical
  follow-up for the same set of tumour samples. The package covers data import from
  the Genomic Data Commons, cBioPortal and local quantification files; quality control
  and filtering; normalisation; differential expression through DESeq2, edgeR or limma-voom
  behind one interface; gene-set enrichment and over-representation testing; Kaplan-Meier
  and Cox survival modelling including genome-wide survival screens; mutation and
  copy-number summarisation; integration of genomic alterations with expression; and
  publication-ready visualisation. Every analysis is recorded in the object so that
  a complete study can be reproduced from one object.
authors:
- family-names: Ahmad
  given-names: Umar
  email: babasaraki@yahoo.co.uk
  orcid: https://orcid.org/0000-0002-3216-5171
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/babasaraki/OncoSeq
commit: 0675d14d3025d43abed9aa6643f6b869414a05a2
url: https://github.com/babasaraki/OncoSeq
date-released: '2026-10-21'
contact:
- family-names: Ahmad
  given-names: Umar
  email: babasaraki@yahoo.co.uk
  orcid: https://orcid.org/0000-0002-3216-5171