Package: SigCheck 2.39.1

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

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SigCheck.pdf |SigCheck.html✨
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-2.39.1(bioc 3.21)SigCheck-2.38.0(bioc 3.20)

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

geneexpressionclassificationgenesetenrichment

3.00 score 1 scripts 202 downloads 1 mentions 6 exports 124 dependencies

Last updated 1 months agofrom:8c0826142e. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 20 2025
R-4.5-winNOTEMar 20 2025
R-4.5-macNOTEMar 20 2025
R-4.5-linuxNOTEMar 20 2025
R-4.4-winNOTEMar 20 2025
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Exports:sigChecksigCheckAllsigCheckKnownsigCheckPermutedsigCheckPlotsigCheckRandom

Dependencies:abindannotateAnnotationDbiaskpassassertthatbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbslibcachemclasscliclustercodetoolscommonmarkcpp11crayoncrosstalkcurlDBIDelayedArrayDEoptimRdigestdiptestdplyre1071evaluatefansifastmapflexmixfontawesomeformatRfpcfsfutile.loggerfutile.optionsgbmgdatagenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggvisgluegtoolshighrhtmltoolshtmlwidgetshttpuvhttrhwriterigraphIRangesjquerylibjsonliteKEGGRESTkernlabknitrlambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimemlbenchMLInterfacesmodeltoolsnnetopensslpillarpkgconfigplogrplspngprabcluspromisesproxyR6rappdirsRColorBrewerRcpprlangrmarkdownrobustbaserpartRSQLiteS4ArraysS4VectorssasssfsmiscshinysnowsourcetoolsSparseArraySummarizedExperimentsurvivalsysthreejstibbletidyselecttinytexUCSC.utilsutf8vctrswithrxfunXMLxtableXVectoryaml

Checking gene expression signatures against random and known signatures with SigCheck

Rendered fromSigCheck.Rnwusingutils::Sweaveon Mar 20 2025.

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