Package: signifinder 1.7.0
signifinder: Collection and implementation of public transcriptional cancer signatures
signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains more than 60 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.
Authors:
signifinder_1.7.0.tar.gz
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signifinder.pdf |signifinder.html✨
signifinder/json (API)
NEWS
# Install 'signifinder' in R: |
install.packages('signifinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/caluralab/signifinder/issues
- ovse - Example expression data.
On BioConductor:signifinder-1.7.0(bioc 3.20)signifinder-1.6.0(bioc 3.19)
Last updated 2 months agofrom:ab19d3b390
Exports:ADOSignAPMSignASCSignautophagySignavailableSignaturesbreastStateSigncellCycleSignchemokineSignCINSignCISSignCombinedSignconsensusOVSigncorrelationSignPlotCOXISSignDNArepSignECMSignEMTSignevaluationSignPlotexpandedImmuneSignferroptosisSigngeneHeatmapSignPlotgetSignGenesglioCellStateSignglycolysisSignheatmapSignPlotHRDSSignhypoxiaSignICBResponseSignIFNSignimmuneCytSignimmunoScoreSignIPRESSignIPSOVSignIPSSignIRGSignISCSignlipidMetabolismSignLRRC15CAFSignmatrisomeSignmelStateSignMITFlowPTENnegSignmitoticIndexSignMPSSignmultipleSignoneSignPlotPassONSignpyroptosisSignridgelineSignPlotstemCellCD49fSignsurvivalSignPlotTGFBSignTinflamSignTLSSignVEGFSign
Dependencies:abindAIMSamapannotateAnnotationDbiAnnotationFilteraskpassassertthatbabelgenebackportsbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiocSetBiocSingularbiomaRtBiostringsbitbit64bitopsblobbootbootstrapbroombslibcachemcarcarDatacheckmatecirclizeclassclicliprclueclustercodetoolscolorspacecommonmarkComplexHeatmapconsensusOVcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirDerivDGEobjDGEobj.utilsdiagramdigestdoBydoParalleldplyre1071edgeRensembldbevaluateexactRankTestsfansifarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygdatagenefugenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggpubrggrepelggridgesggsciggsignifggtextGlobalOptionsglobalsgluegraphgridExtragridtextGSEABaseGSVAgtablegtoolsHDF5Arrayhexbinhighrhmshtmltoolshtmlwidgetshttrhttr2iC10iC10TrainingDataimputeinterpipredIRangesirlbaisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothkm.ciKMsurvknitrlabelinglambda.rlaterlatticelatticeExtralavalazyevallifecyclelimmalistenvlme4locfitlubridatemagickmagrittrmapprojmapsmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmclustmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivontologyIndexopenairopensslorg.Hs.eg.dbpamrparallellypatchworkpbkrtestpillarpkgconfigplogrplotlyplyrpngpolynomprettyunitsprodlimprogressprogressrpromisesProtGenericsproxypurrrquantregR6randomForestrappdirsRColorBrewerRcppRcppEigenRCurlreadrrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrmetarpartRsamtoolsRSQLiterstatixrsvdrtracklayerS4ArraysS4VectorssassScaledMatrixscalesshapeSingleCellExperimentsnowsparrowSparseArraySparseMsparseMatrixStatsSpatialExperimentSQUAREMstatmodstringistringrSummarizedExperimentSuppDistssurvcompsurvivalsurvivalROCsurvminersurvMiscsystibbletidyrtidyselecttimechangetinytexTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGenetzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioczoo