Package: signifinder 1.14.0

Stefania Pirrotta

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 coming from public literature, based on gene expression values, and return single-sample (-cell/-spot) scores. Currently, signifinder collects more than 70 distinct signatures, relating to multiple tumors and multiple cancer processes.

Authors:Stefania Pirrotta [cre, aut], Enrica Calura [aut]

signifinder_1.14.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
signifinder/json (API)
NEWS

# Install 'signifinder' in R:
install.packages('signifinder', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/caluralab/signifinder/issues

Datasets:
  • ovse - Example expression data.

On BioConductor:signifinder-1.15.0(bioc 3.24)signifinder-1.13.0(bioc 3.23)

geneexpressiongenetargetimmunooncologybiomedicalinformaticsrnaseqmicroarrayreportwritingvisualizationsinglecellspatialgenesignaling

4.76 score 9 stars 16 scripts 339 downloads 58 exports 245 dependencies

Last updated from:e7ce92113c (on RELEASE_3_23). Checks:1 NOTE, 8 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE349
linux-devel-x86_64ERROR998
source / vignettesERROR554
linux-release-x86_64ERROR1020
macos-release-arm64ERROR552
macos-oldrel-arm64ERROR720
windows-develERROR939
windows-releaseERROR1014
windows-oldrelERROR981
wasm-releaseOK306

Exports:ADOSignAPMSignASCSignautophagySignavailableSignaturesCD39CD8TcellSigncellCycleSignchemokineSignCINSignCISSignCombinedSignconsensusOVSigncorrelationSignPlotCOXISSignDNArepSignECMSignEMTSignevaluationSignPlotexpandedImmuneSignferroptosisSigngeneHeatmapSignPlotgetSignGenesglycolysisSignheatmapSignPlotHRDSSignhypoxiaSignICBResponseSignIFNSignimmuneCytSignimmunoScoreSigninterferonSignIPRESSignIPSOVSignIPSSignIRGSignISCSignlipidMetabolismSignLRRC15CAFSignmatrisomeSignmetalSignMITFlowPTENnegSignmitoticIndexSignMPSSignmultipleSignoneSignPlotoxphosSignPassONSignpyroptosisSignridgelineSignPlotSCSubtypeSignstateSignstemCellCD49fSignstressSignsurvivalSignPlotTGFBSignTinflamSignTLSSignVEGFSign

Dependencies:abindAIMSamapannotateAnnotationDbiAnnotationFilteraskpassassertthatassortheadbackportsbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelBiocSingularbiomaRtBiostringsbitbit64bitopsblobbootbootstrapbroomcachemcarcarDatacigarillocirclizeclassclicliprclueclustercodetoolscolorspacecommonmarkComplexHeatmapconsensusOVcorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsDerivDGEobjDGEobj.utilsdiagramdigestdir.expirydoBydoParalleldplyre1071ensembldbexactRankTestsfarverfastmapfilelockforeachforecastformatRFormulafracdifffutile.loggerfutile.optionsfuturefuture.applygdatagenefugenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2ggpubrggrepelggridgesggsciggsignifggtextGlobalOptionsglobalsgluegraphgridExtragridtextGSEABaseGSVAgtablegtoolsh5mreadHDF5Arrayhmshttrhttr2iC10iC10TrainingDataimputeipredIRangesirlbaisobanditeratorsjpegjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelavalazyevallifecyclelimmalistenvlitedownlme4lmtestlubridatemagickmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmclustmemoisememusemgcvmicrobenchmarkmimeminqamodelrmvtnormnlmenloptrnnetnumDerivopenairopensslorg.Hs.eg.dbpamrparallellypatchworkpbkrtestpillarpkgconfigpngpolynomprettyunitsprodlimprogressprogressrProtGenericsproxypurrrquantregR6randomForestrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreformulasrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmetarpartRsamtoolsRSQLiterstatixrsvdrtracklayerS4ArraysS4VectorsS7ScaledMatrixscalesSeqinfoshapeSingleCellExperimentsnowSparseArraySparseMsparseMatrixStatsSpatialExperimentSQUAREMstatmodstringistringrSummarizedExperimentSuppDistssurvcompsurvivalsurvivalROCsurvminersystibbletidyrtidyselecttimechangetimeDateTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGenetzdbUCSC.utilsurcautf8vctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzoo

Readme and manuals

Help Manual

Help pageTopics
Adenosine Signaling SignatureADOSign
Antigen Processing Machinery SignatureAPMSign
Adult Stem Cell SignatureASCSign
Autophagy SignatureautophagySign
Show Available SignaturesavailableSignatures
CD39+ CD8+ T cells SignatureCD39CD8TcellSign
Cell-cycle Signature classifiercellCycleSign
Chemokine SignaturechemokineSign
Chromosomal instability SignatureCINSign
CIS (carcinoma-in situ) SignatureCISSign
EMT-Inflammation Combined SignatureCombinedSign
ConsensusOV SignatureconsensusOVSign
Correlation PlotcorrelationSignPlot
COX-2-associated Inflammatory SignatureCOXISSign
DNA Repair SignatureDNArepSign
Extracellular Matrix SignatureECMSign
Epithelial-Mesenchymal Transition SignatureEMTSign
Evaluation PlotevaluationSignPlot
ExpandedImmune SignatureexpandedImmuneSign
Ferroptosis SignatureferroptosisSign
Genes' Signatures' HeatmapgeneHeatmapSignPlot
Get Signature Gene ListgetSignGenes
Glycolysis SignatureglycolysisSign
Global Heatmap of Signatures' scores.heatmapSignPlot
Homologous Recombination Deficiency SignatureHRDSSign
Hypoxia SignaturehypoxiaSign
ICB Response SignatureICBResponseSign
IFN-gamma SignatureIFNSign
Immune Cytolytic Activity SignatureimmuneCytSign
Immunogenic SignatureimmunoScoreSign
Interferon SignatureinterferonSign
IPRES SignatureIPRESSign
IPSOV SignatureIPSOVSign
ImmunoPhenoScore SignatureIPSSign
Immune-Related Genes SignatureIRGSign
Adult Intestinal Stem Cell SignatureISCSign
Lipid Metabolism SignaturelipidMetabolismSign
LRRC15 CAF SignatureLRRC15CAFSign
Core Matrisome Gene signaturematrisomeSign
Metal Response SignaturemetalSign
MITFlow/PTENneg SignatureMITFlowPTENnegSign
Mitotic IndexmitoticIndexSign
Melanocytic Plasticity SignatureMPSSign
Multiple Signatures ComputationmultipleSign
Scatterplot for a single signatureoneSignPlot
Example expression data.ovse
Oxidative Phosphorylation SignatureoxphosSign
passON SignaturePassONSign
Pyroptosis SignaturepyroptosisSign
Ridgeline PlotridgelineSignPlot
Breast Cancer Subtypes SignatureSCSubtypeSign
Cellular States SignaturestateSign
CD49fHi Basal Stem Cell SignaturestemCellCD49fSign
Stress Response SignaturestressSign
Survival PlotsurvivalSignPlot
Pan-Fibroblast TGFB Response SignatureTGFBSign
TinflamSign SignatureTinflamSign
Tertiary Lymphoid Structures (TLS) SignatureTLSSign
VEGF SignatureVEGFSign