Package: SigCheck 2.37.0
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:
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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')) |
- classifyResults - Precomputed list of results for a calls to 'sigCheckRandom' and 'sigCheckKnown' using the 'breastCancerNKI' dataset.
- 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-2.37.0(bioc 3.20)SigCheck-2.36.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:20d4426795
Exports:sigChecksigCheckAllsigCheckKnownsigCheckPermutedsigCheckPlotsigCheckRandom
Dependencies:abindannotateAnnotationDbiaskpassassertthatbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobbslibcachemclasscliclustercodetoolscommonmarkcpp11crayoncrosstalkcurlDBIDelayedArrayDEoptimRdigestdiptestdplyre1071evaluatefansifastmapflexmixfontawesomeformatRfpcfsfutile.loggerfutile.optionsgbmgdatagenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggvisgluegtoolshighrhtmltoolshtmlwidgetshttpuvhttrhwriterigraphIRangesjquerylibjsonliteKEGGRESTkernlabknitrlambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimemlbenchMLInterfacesmodeltoolsnnetopensslpillarpkgconfigplogrplspngprabcluspromisesproxyR6rappdirsRColorBrewerRcpprlangrmarkdownrobustbaserpartRSQLiteS4ArraysS4VectorssasssfsmiscshinysnowsourcetoolsSparseArraySummarizedExperimentsurvivalsysthreejstibbletidyselecttinytexUCSC.utilsutf8vctrswithrxfunXMLxtableXVectoryamlzlibbioc
