Package: OncoSeq
Type: Package
Title: End-to-End Analysis of Cancer Transcriptomes and Genomes
Version: 0.99.1
Authors@R: person(given = "Umar", family = "Ahmad",
    email = "babasaraki@yahoo.co.uk", role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-3216-5171"))
Description: 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.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.4.0), SummarizedExperiment
Imports: methods, stats, utils, grDevices, S4Vectors, DESeq2, edgeR,
        limma, fgsea, BiocParallel, survival, ggplot2, ggrepel,
        matrixStats, httr2, jsonlite
Suggests: TCGAbiolinks, maftools, clusterProfiler, org.Hs.eg.db,
        ComplexHeatmap, pheatmap, survminer, tximport, msigdbr, apeglm,
        testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
biocViews: Software, GeneExpression, DifferentialExpression, RNASeq,
        Transcriptomics, Sequencing, GeneSetEnrichment, Survival,
        SomaticMutation, CopyNumberVariation, Visualization,
        QualityControl, DataImport, Normalization, MultipleComparison
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://github.com/babasaraki/OncoSeq
BugReports: https://github.com/babasaraki/OncoSeq/issues
Collate: 'AllGenerics.R' 'AllClasses.R' 'methods-OncoSeqExperiment.R'
        'utils.R' 'import-local.R' 'import-gdc.R' 'import-cbioportal.R'
        'qc.R' 'normalize.R' 'de.R' 'genesets.R' 'enrichment.R'
        'mutations.R' 'cnv.R' 'survival.R' 'integrate.R' 'plots.R'
        'pipeline.R' 'data.R' 'zzz.R'
Config/roxygen2/version: 8.1.1
NeedsCompilation: no
Config/pak/sysreqs: libssl-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-21 04:29:39 UTC
RemoteUrl: https://github.com/BiocStaging/OncoSeq
RemoteRef: HEAD
RemoteSha: 0675d14d3025d43abed9aa6643f6b869414a05a2
Packaged: 2026-10-21 06:21:27 UTC; root
Author: Umar Ahmad [aut, cre] (ORCID: <https://orcid.org/0000-0002-3216-5171>)
Maintainer: Umar Ahmad <babasaraki@yahoo.co.uk>