Package: OUTRIDER 1.31.0

Christian Mertes

OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

Identification of aberrant gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore, OUTRIDER provides useful plotting functions to analyze and visualize the results.

Authors:Felix Brechtmann [aut], Christian Mertes [aut, cre], Agne Matuseviciute [aut], Michaela Fee Müller [ctb], Andrea Raithel [ctb], Vicente Yepez [aut], Julien Gagneur [aut]

OUTRIDER_1.31.0.tar.gz
OUTRIDER_1.31.0.zip(r-4.7)OUTRIDER_1.31.0.zip(r-4.6)OUTRIDER_1.31.0.zip(r-4.5)
OUTRIDER_1.31.0.tgz(r-4.6-x86_64)OUTRIDER_1.31.0.tgz(r-4.6-arm64)OUTRIDER_1.31.0.tgz(r-4.5-x86_64)OUTRIDER_1.31.0.tgz(r-4.5-arm64)
OUTRIDER_1.31.0.tar.gz(r-4.7-arm64)OUTRIDER_1.31.0.tar.gz(r-4.7-x86_64)OUTRIDER_1.31.0.tar.gz(r-4.6-arm64)OUTRIDER_1.31.0.tar.gz(r-4.6-x86_64)
OUTRIDER_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OUTRIDER/json (API)
NEWS

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

Bug tracker:https://github.com/gagneurlab/outrider/issues

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

On BioConductor:OUTRIDER-1.31.0(bioc 3.24)OUTRIDER-1.30.0(bioc 3.23)

immunooncologyrnaseqtranscriptomicsalignmentsequencinggeneexpressiongeneticscount-datadiagnosticsexpression-analysismendelian-geneticsoutlier-detectionrna-seqopenblascpp

8.52 score 56 stars 1 packages 167 scripts 674 downloads 3 mentions 45 exports 162 dependencies

Last updated from:f5f7a6b9de. Checks:12 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING297
linux-devel-arm64WARNING534
linux-devel-x86_64WARNING631
source / vignettesERROR711
linux-release-arm64WARNING500
linux-release-x86_64WARNING547
macos-release-arm64WARNING322
macos-release-x86_64WARNING666
macos-oldrel-arm64WARNING270
macos-oldrel-x86_64WARNING732
windows-develWARNING666
windows-releaseWARNING743
windows-oldrelWARNING731
wasm-releaseOK256

Exports:aberrantcomputeGeneLengthcomputeLatentSpacecomputePvaluescomputeZscorescontrolForConfounderscountscounts<-dispersionsestimateBestQestimateSizeFactorsfilterExpressionfindInjectZscorefitfpkmfpmgetBestQmakeExampleOutriderDataSetnormalizationFactorsnormalizationFactors<-OUTRIDEROutriderDataSetpadjplotAberrantPerSampleplotCountCorHeatmapplotCountGeneSampleHeatmapplotDispEstsplotEncDimSearchplotExpectedVsObservedCountsplotExpressedGenesplotExpressionRankplotFPKMplotManhattanplotPowerAnalysisplotQQplotSizeFactorsplotVolcanopValueresultssampleExclusionMasksampleExclusionMask<-sizeFactorssizeFactors<-thetazScore

Dependencies:abindAnnotationDbiaskpassassertthatbackportsbase64encBBmiscBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcacachemcallrcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestdplyreggevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggrepelgluegridExtragtableheatmaplyhighrhmshtmltoolshtmlwidgetshttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslotelpcaMethodspermutepheatmappillarpkgconfigplotlyplyrpngpracmaprettyunitsprocessxprogresspromisesPRROCpspurrrqapR6rappdirsRColorBrewerRcppRcppArmadilloRCurlregistryreshape2restfulrRhtslibrjsonrlangrmarkdownRMTstatRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesSeqinfoseriationsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexTSPtxdbmakerUCSC.utilsutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxml2XVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Number of aberrant eventsaberrant aberrant,OutriderDataSet-method
Extracting the gene length from annotationscomputeGeneLength
Extracting the latent spacecomputeLatentSpace
Calculate P-valuescomputePvalues computePvalues,OutriderDataSet-method
Z score computationcomputeZscores computeZscores,OutriderDataSet-method
Autoencoder function to correct for confounders.controlForConfounders
Accessors for the 'counts' slot of an OutriderDataSet object.counts counts,OutriderDataSet-method counts<-,OutriderDataSet,matrix-method
Find the optimal encoding dimensionestimateBestQ estimateBestQ, findInjectZscore
Filter expressionfilterExpression filterExpression,OutriderDataSet-method
Fit the negative binomial distributionfit fit.OutriderDataSet
Calculate FPM and FPKM valuesfpkm fpm
Getter/Setter functionsdispersion, dispersions dispersions,OutriderDataSet-method getBestQ getter_setter_functions padj padj, pValue pValue, theta theta, zScore zScore,
Create example data sets for OUTRIDERmakeExampleOutriderDataSet
Accessor functions for the normalization factors in an OutriderDataSet object.normalizationFactors normalizationFactors,OutriderDataSet-method normalizationFactors<-,OutriderDataSet,data.frame-method normalizationFactors<-,OutriderDataSet,DataFrame-method normalizationFactors<-,OutriderDataSet,matrix-method normalizationFactors<-,OutriderDataSet,NULL-method
OUTRIDER - Finding expression outlier eventsOUTRIDER
OutriderDataSet class and constructorsOutriderDataSet OutriderDataSet-class
Visualization functions for OUTRIDERplotAberrantPerSample plotAberrantPerSample,OutriderDataSet-method plotCountCorHeatmap plotCountCorHeatmap,OutriderDataSet-method plotCountGeneSampleHeatmap plotDispEsts plotDispEsts,OutriderDataSet-method plotEncDimSearch plotEncDimSearch,OutriderDataSet-method plotExpectedVsObservedCounts plotExpressedGenes plotExpressionRank plotFPKM plotFunction plotFunctions plotManhattan plotManhattan,OutriderDataSet-method plotPowerAnalysis plotQQ plotQQ,OutriderDataSet-method plotSizeFactors plotVolcano plotVolcano,OutriderDataSet-method
Accessor function for the 'results' object in an OutriderDataSet object.results results,OutriderDataSet-method
Sample exclusionsampleExclusionMask sampleExclusionMask, sampleExclusionMask<- `sampleExclusionMask<-`
SizeFactors accessor and estimation functionestimateSizeFactors estimateSizeFactors,OutriderDataSet-method sizeFactors sizeFactors,OutriderDataSet-method sizeFactors<- sizeFactors<-,OutriderDataSet,NULL-method sizeFactors<-,OutriderDataSet,numeric-method