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-2.39.0(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 208 downloads 1 mentions 6 exports 124 dependencies

Last updated 17 hours agofrom:8c0826142e. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 15 2025
R-4.5-winNOTEFeb 15 2025
R-4.5-macWARNINGFeb 15 2025
R-4.5-linuxNOTEFeb 15 2025
R-4.4-winNOTEFeb 15 2025
R-4.4-macNOTEFeb 15 2025
R-4.3-winNOTEFeb 15 2025
R-4.3-macNOTEFeb 15 2025

Exports:sigChecksigCheckAllsigCheckKnownsigCheckPermutedsigCheckPlotsigCheckRandom

Dependencies:abindannotateAnnotationDbiaskpassassertthatbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbslibcachemclasscliclustercodetoolscommonmarkcpp11crayoncrosstalkcurlDBIDelayedArrayDEoptimRdigestdiptestdplyre1071evaluatefansifastmapflexmixfontawesomeformatRfpcfsfutile.loggerfutile.optionsgbmgdatagenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggvisgluegtoolshighrhtmltoolshtmlwidgetshttpuvhttrhwriterigraphIRangesjquerylibjsonliteKEGGRESTkernlabknitrlambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimemlbenchMLInterfacesmodeltoolsnnetopensslpillarpkgconfigplogrplspngprabcluspromisesproxyR6rappdirsRColorBrewerRcpprlangrmarkdownrobustbaserpartRSQLiteS4ArraysS4VectorssasssfsmiscshinysnowsourcetoolsSparseArraySummarizedExperimentsurvivalsysthreejstibbletidyselecttinytexUCSC.utilsutf8vctrswithrxfunXMLxtableXVectoryaml

Checking gene expression signatures against random and known signatures with SigCheck

Rendered fromSigCheck.Rnwusingutils::Sweaveon Feb 15 2025.

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