Package: SigCheck 2.39.0

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

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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'))

Peer review:

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

3.30 score 1 scripts 233 downloads 1 mentions 6 exports 125 dependencies

Last updated 2 months agofrom:c6bed0cd3f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winNOTEDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winNOTEDec 19 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winNOTEDec 19 2024
R-4.3-macNOTEDec 19 2024

Exports:sigChecksigCheckAllsigCheckKnownsigCheckPermutedsigCheckPlotsigCheckRandom

Dependencies:abindannotateAnnotationDbiaskpassassertthatbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbslibcachemclasscliclustercodetoolscommonmarkcpp11crayoncrosstalkcurlDBIDelayedArrayDEoptimRdigestdiptestdplyre1071evaluatefansifastmapflexmixfontawesomeformatRfpcfsfutile.loggerfutile.optionsgbmgdatagenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggvisgluegtoolshighrhtmltoolshtmlwidgetshttpuvhttrhwriterigraphIRangesjquerylibjsonliteKEGGRESTkernlabknitrlambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimemlbenchMLInterfacesmodeltoolsnnetopensslpillarpkgconfigplogrplspngprabcluspromisesproxyR6rappdirsRColorBrewerRcpprlangrmarkdownrobustbaserpartRSQLiteS4ArraysS4VectorssasssfsmiscshinysnowsourcetoolsSparseArraySummarizedExperimentsurvivalsysthreejstibbletidyselecttinytexUCSC.utilsutf8vctrswithrxfunXMLxtableXVectoryamlzlibbioc

Checking gene expression signatures against random and known signatures with SigCheck

Rendered fromSigCheck.Rnwusingutils::Sweaveon Dec 19 2024.

Last update: 2022-12-09
Started: 2022-12-09