Package: SigCheck 2.45.0

Rory Stark

SigCheck: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

While gene signatures are frequently used to predict phenotypes (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours' paper "Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome"). Based on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata.

Authors:Rory Stark <[email protected]> and Justin Norden

SigCheck_2.45.0.tar.gz
SigCheck_2.45.0.zip(r-4.7)SigCheck_2.45.0.zip(r-4.6)SigCheck_2.45.0.zip(r-4.5)
SigCheck_2.45.0.tgz(r-4.6-any)SigCheck_2.45.0.tgz(r-4.5-any)
SigCheck_2.45.0.tar.gz(r-4.7-any)SigCheck_2.45.0.tar.gz(r-4.6-any)
SigCheck_2.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SigCheck/json (API)
NEWS

# Install 'SigCheck' in R:
install.packages('SigCheck', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • knownSignatures - Previously identified gene signatures for use in 'sigCheckKnown'
  • nkiResults - Precomputed list of results for a call to 'sigCheckAll' using the 'breastCancerNKI' dataset.

On BioConductor:SigCheck-2.45.0(bioc 3.24)SigCheck-2.44.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressionclassificationgenesetenrichment

3.30 score 4 scripts 364 downloads 1 mentions 6 exports 121 dependencies

Last updated from:0a23557023. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR204
linux-devel-x86_64NOTE458
source / vignettesOK275
linux-release-x86_64NOTE485
macos-release-arm64NOTE352
macos-oldrel-arm64NOTE270
windows-develNOTE359
windows-releaseNOTE484
windows-oldrelNOTE365
wasm-releaseOK161

Exports:sigChecksigCheckAllsigCheckKnownsigCheckPermutedsigCheckPlotsigCheckRandom

Dependencies:abindannotateAnnotationDbiaskpassassertthatbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbslibcachemclasscliclustercodetoolscommonmarkcpp11crayoncrosstalkcurlDBIDelayedArrayDEoptimRdigestdiptestdplyre1071evaluatefastmapflexmixfontawesomeformatRfpcfsfutile.loggerfutile.optionsgbmgdatagenefiltergenericsGenomicRangesggvisgluegtoolshighrhtmltoolshtmlwidgetshttpuvhttrhwriterigraphIRangesjquerylibjsonliteKEGGRESTkernlabknitrlambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimemlbenchMLInterfacesmodeltoolsnnetopensslotelpillarpkgconfigplspngprabcluspromisesproxyR6rappdirsRColorBrewerRcpprlangrmarkdownrobustbaserpartRSQLiteS4ArraysS4VectorssassSeqinfosfsmiscshinysnowsourcetoolsSparseArraySummarizedExperimentsurvivalsysthreejstibbletidyselecttinytexutf8vctrswithrxfunXMLxtableXVectoryaml

Checking gene expression signatures against random and known signatures with SigCheck

Rendered fromSigCheck.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2025-02-14
Started: 2022-12-09