Package: signeR 2.15.0

Renan Valieris

signeR: Empirical Bayesian approach to mutational signature discovery

The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.

Authors:Rafael Rosales, Rodrigo Drummond, Renan Valieris, Alexandre Defelicibus, Israel Tojal da Silva

signeR_2.15.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
signeR/json (API)

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

Bug tracker:https://github.com/tojallab/signer/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:signeR-2.15.0(bioc 3.24)signeR-2.14.0(bioc 3.23)

genomicvariationsomaticmutationstatisticalmethodvisualizationbioconductorbioinformaticsopenblascpp

7.88 score 14 stars 25 scripts 9 mentions 31 exports 231 dependencies

Last updated from:2d8d6b1223. Checks:1 ERROR, 11 NOTE, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR391
linux-devel-arm64NOTE555
linux-devel-x86_64NOTE762
source / vignettesOK740
linux-release-arm64NOTE555
linux-release-x86_64NOTE694
macos-release-arm64NOTE332
macos-release-x86_64NOTE639
macos-oldrel-arm64NOTE349
macos-oldrel-x86_64NOTE740
windows-develNOTE635
windows-releaseNOTE586
windows-oldrelNOTE584
wasm-releaseFAIL300

Exports:Average_expAverage_signBICboxplotDiffExpExposureBarplotExposureBoxplotExposureClassifyExposureClassifyCVExposureCorrelationExposureGLMExposureHeatExposureSurvivalExposureSurvModelFuzzyClustExpgenCountMatrixFromMAFgenCountMatrixFromVcfgenOpportunityFromGenomeHClustExpMedian_expMedian_signNormalizePathsReorder_mutationsReorder_samplesReorder_signaturessetMutationssetSamplessigneRsigneRFlowSignHeatSignPlot

Dependencies:abindadaAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbootbroomBSgenomebslibbsplusBWStestcachemcarcarDatacigarilloclassclicliprclueclustercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurlDBIdbplyrDelayedArrayDerivdigestdoBydoParalleldplyrDTe1071evaluateexactRankTestsfarverfastmapfilelockfontawesomeforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggpubrggrepelggsciggsignifggtextglmnetglobalsgluegmpgridBasegridExtragridtextgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphinaparcIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTkknnknitrkpeakskSampleslabelinglambda.rlaterlatticelazyevallhslifecyclelistenvlitedownlme4lmtestlubridatemagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmemoisemgcvmimeminqamodelrmultcompViewmvtnormnlmenloptrNMFnnetnumDerivopensslotelparallellypbkrtestpheatmappillarpkgconfigplyrPMCMRpluspngpolynomppclustprettyunitspROCprogresspromisesproxypurrrpvclustquantregR6randomForestrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreformulasregistryreshape2restfulrRhtslibrjsonrlangrmarkdownRmpfrrngtoolsrpartRsamtoolsRSQLiterstatixrtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshapeshinyshinycssloadersshinydashboardshinyWidgetssnowsourcetoolsSparseArraySparseMstringistringrSummarizedExperimentSuppDistssurvivalsurvminersystibbletidyrtidyselecttimechangetimeDatetinytextzdbUCSC.utilsurcautf8VariantAnnotationvctrsVGAMviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzoo

signeR
1: Introduction | 2: Installation | 3: Preparing the input | 4: Estimating the number of mutational processes and their signatures | 5: Estimating exposures to known signatures. | 6: Results and plots | 7: Supervised approaches to exposure analysis | 8: Unsupervised approaches to exposure analysis | 9: Frequently Asked Questions | 10: References | Debug Info
Rendered fromsigneR-vignette.Rhtmlusingknitr::knitr

Last update: 2023-10-18
Started: 2016-09-12

signeRFlow
Introduction | Install signeR | Running shiny app | Modules | signeR de novo | Load data | VCF, MAF or SNV Matrix | Opportunity matrix | de novo analysis | cosmic cosine | signeR fitting | SNV matrix | Previous signatures | Fitting analysis | Downstream analysis | Clustering | Covariate | TCGA Explorer | Filter dataset | Covariate analysis | SessionInfo
Rendered fromsigneRFlow.Rmdusingknitr::rmarkdown

Last update: 2023-10-16
Started: 2022-07-13

Readme and manuals

Help Manual

Help pageTopics
Empirical Bayesian approach to mutational signature discoverysigneR-package
COSMIC Mutational Signaturescosmic_data
Differential Exposure AnalysisDiffExp DiffExp,SignExp,character-method
Classify samples by exposure levelsExposureClassify ExposureClassify,ANY,character-method ExposureClassify,SignExp,character-method
k-fold cross-validation of sample classifcation by exposure levelsExposureClassifyCV ExposureClassifyCV,ANY,character-method ExposureClassifyCV,SignExp,character-method
Exposure correlation analysis (given a known sample feature)ExposureCorrelation ExposureCorrelation,matrix,numeric-method ExposureCorrelation,SignExp,numeric-method
Exposure Generalized Linear ModelExposureGLM ExposureGLM,matrix,numeric-method ExposureGLM,SignExp,numeric-method
Exposure survival analysisExposureSurvival ExposureSurvival,matrix,character-method ExposureSurvival,matrix,Surv-method ExposureSurvival,matrix-method ExposureSurvival,SignExp,character-method ExposureSurvival,SignExp,Surv-method ExposureSurvival,SignExp-method
Exposure Cox modelExposureSurvModel ExposureSurvModel,matrix,character-method ExposureSurvModel,matrix,Surv-method ExposureSurvModel,matrix-method ExposureSurvModel,SignExp,character-method ExposureSurvModel,SignExp,Surv-method ExposureSurvModel,SignExp-method
Fuzzy Clustering of exposure dataFuzzyClustExp FuzzyClustExp,SignExp,numeric-method FuzzyClustExp,SignExp-method
count matrix and opportunity matrix generatorsgenCountMatrixFromMAF genCountMatrixFromVcf genOpportunityFromGenome
Hierarchical Clustering of exposure dataHClustExp HClustExp,SignExp,numeric-method HClustExp,SignExp-method
SignExp class methodsAverage_exp Average_exp,SignExp-method Average_sign Average_sign,SignExp-method Median_exp Median_exp,SignExp-method Median_sign Median_sign,SignExp-method Normalize Normalize,SignExp-method Reorder_mutations Reorder_mutations,SignExp,numeric-method Reorder_samples Reorder_samples,SignExp,numeric-method Reorder_signatures Reorder_signatures,SignExp,numeric-method setMutations setMutations,SignExp-method setSamples setSamples,SignExp-method
signeR plot functionsBICboxplot ExposureBarplot ExposureBarplot,SignExp-method ExposureBoxplot ExposureBoxplot,SignExp-method ExposureHeat ExposureHeat,SignExp-method Paths Paths,SignExp-method SignHeat SignHeat,SignExp-method SignPlot SignPlot,SignExp-method
signeRsigneR
Launch signeRFlow R Shiny web appsigneRFlow
SignExp classSignExp SignExp-class
TCGA Cosmic similaritiestcga_similarities
TCGA tumors used on TCGA Explorertcga_tumors