Package: OncoSeq 0.99.1

Umar Ahmad

OncoSeq: End-to-End Analysis of Cancer Transcriptomes and Genomes

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:Umar Ahmad [aut, cre]

OncoSeq_0.99.1.tar.gz
OncoSeq_0.99.1.zip(r-4.7-any)OncoSeq_0.99.1.zip(r-4.6-any)OncoSeq_0.99.1.zip(r-4.5-any)
OncoSeq_0.99.1.tgz(r-4.6-any)OncoSeq_0.99.1.tgz(r-4.5-any)
OncoSeq_0.99.1.tar.gz(r-4.7-any)OncoSeq_0.99.1.tar.gz(r-4.6-any)
OncoSeq_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OncoSeq/json (API)

# Install 'OncoSeq' in R:

install.packages('OncoSeq', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/babasaraki/oncoseq/issues

Datasets:

blcaExample - Bladder urothelial carcinoma multi-omic example cohort
simExample - Simulated cancer multi-omic cohort

On CRAN:

software geneexpression differentialexpression rnaseq transcriptomics sequencing genesetenrichment survival somaticmutation copynumbervariation visualization qualitycontrol dataimport normalization multiplecomparison

2.70 score 53 exports 62 dependencies

Last updated from:0675d14d30. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	218
linux-devel	OK	390
source / vignettes	OK	632
linux-release	OK	482
macos-release	OK	293
macos-oldrel	OK	298
windows-devel	OK	305
windows-release	OK	350
windows-oldrel	OK	283
wasm-release	OK	234

Exports:alignLayers analyses analyses<-asOncoSeq cbioProfiles cbioStudies cnv cnv<-cnvExpressionCorrelation cnvFrequency cnvSummary compareEngines coxModel detectOutliers diffExpress exampleOncoSeq filterLowExpression getAnalysis importCBioPortal importCounts importGDC importMAF importTximport integrateMutationExpression msigdbrSets mutationFrequency mutations mutations<-mutationStatus mutationSummary normalizeCounts oncoplotData OncoSeqExperiment plotCNVFrequency plotEnrichmentBar plotExpressionHeatmap plotKM plotMAplot plotMutationFrequency plotOncoprint plotSamplePCA plotVolcano provenance provenance<-qcMetrics readGMT runGSEA runOncoSeq runORA show survivalFit survivalScreen tumourMutationBurden

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel cli codetools cowplot cpp11 curl data.table DelayedArray DESeq2 edgeR farver fastmatch fgsea formatR futile.logger futile.options generics GenomicRanges ggplot2 ggrepel glue gtable httr2 IRanges isoband jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats openssl R6 RColorBrewer Rcpp RcppArmadillo rlang S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod SummarizedExperiment survival sys vctrs viridisLite withr XVector

Analysing cancer transcriptomes and genomes with OncoSeq

Rendered fromOncoSeq.Rmdusingknitr::rmarkdown

Last update: 2026-10-20
Started: 2026-10-20

Help page	Topics
Restrict an object to samples present in every layer	alignLayers
Convert an existing object to an OncoSeqExperiment	asOncoSeq
Bladder urothelial carcinoma multi-omic example cohort	blcaExample
List the molecular profiles of a cBioPortal study	cbioProfiles
List studies available from cBioPortal	cbioStudies
Correlate copy number with expression	cnvExpressionCorrelation
Copy-number alteration frequency	cnvFrequency
Summarise gene-level copy-number alterations	cnvSummary
Run the same contrast through every engine and compare	compareEngines
Multivariable Cox proportional-hazards model	coxModel
Flag candidate outlier samples	detectOutliers
Differential expression with DESeq2, edgeR or limma	diffExpress
A small simulated cancer multi-omic dataset	exampleOncoSeq
Remove weakly expressed features	filterLowExpression
Retrieve a stored analysis result	getAnalysis
Import a cBioPortal study	importCBioPortal
Import counts and sample annotation from local data	importCounts
Import a TCGA/GDC project	importGDC
Read a MAF file	importMAF
Import transcript-level quantifications through tximport	importTximport
Differential expression between mutant and wild-type tumours	integrateMutationExpression
Fetch a gene-set collection through msigdbr	msigdbrSets
Mutation frequency across the cohort	mutationFrequency
Mutation status of a gene as a factor	mutationStatus
Summarise the somatic mutation layer	mutationSummary
Normalise expression data	normalizeCounts
Build the matrix behind an oncoprint	oncoplotData
OncoSeq generics	analyses analyses<- cnv cnv<- mutations mutations<- OncoSeq-generics provenance provenance<-
Construct an OncoSeqExperiment	OncoSeqExperiment
Container for a cancer multi-omic study	OncoSeqExperiment-class
Methods for OncoSeqExperiment objects	analyses,OncoSeqExperiment-method analyses<-,OncoSeqExperiment-method cnv,OncoSeqExperiment-method cnv<-,OncoSeqExperiment-method mutations,OncoSeqExperiment-method mutations<-,OncoSeqExperiment-method OncoSeqExperiment-methods provenance,OncoSeqExperiment-method provenance<-,OncoSeqExperiment-method show,OncoSeqExperiment-method [,OncoSeqExperiment,ANY,ANY,ANY-method
Copy-number alteration frequency plot	plotCNVFrequency
Bar chart of enrichment results	plotEnrichmentBar
Heatmap of selected features	plotExpressionHeatmap
Kaplan-Meier curves	plotKM
Mean-difference (MA) plot of a differential-expression result	plotMAplot
Mutation frequency plot with confidence intervals	plotMutationFrequency
Oncoprint-style mutation landscape	plotOncoprint
Principal component plot of samples	plotSamplePCA
Volcano plot of a differential-expression result	plotVolcano
Compute per-sample quality-control metrics	qcMetrics
Read a gene-set collection from a GMT file	readGMT
Gene set enrichment analysis on a differential-expression result	runGSEA
Run the full OncoSeq workflow in one call	runOncoSeq
Over-representation analysis of a differentially expressed gene list	runORA
Simulated cancer multi-omic cohort	simExample
Kaplan-Meier analysis of a gene or clinical variable	survivalFit
Genome-wide screen for survival-associated genes	survivalScreen
Tumour mutation burden	tumourMutationBurden

Package: OncoSeq 0.99.1

OncoSeq: End-to-End Analysis of Cancer Transcriptomes and Genomes

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