Package: OUTRIDER 1.25.0

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], Vicente Yepez [aut], Julien Gagneur [aut]

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OUTRIDER.pdf |OUTRIDER.html✨
OUTRIDER/json (API)
NEWS

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

Peer review:

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

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

On BioConductor:OUTRIDER-1.25.0(bioc 3.21)OUTRIDER-1.24.0(bioc 3.20)

immunooncologyrnaseqtranscriptomicsalignmentsequencinggeneexpressiongeneticscount-datadiagnosticsexpression-analysismendelian-geneticsoutlier-detectionrna-seqopenblascpp

9.06 score 49 stars 1 packages 109 scripts 358 downloads 3 mentions 46 exports 160 dependencies

Last updated 2 months agofrom:e21b7d6335. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-win-x86_64NOTEDec 18 2024
R-4.5-linux-x86_64NOTEDec 18 2024
R-4.4-win-x86_64NOTEDec 18 2024
R-4.4-mac-x86_64NOTEDec 18 2024
R-4.4-mac-aarch64NOTEDec 18 2024
R-4.3-win-x86_64NOTEDec 18 2024
R-4.3-mac-x86_64NOTEDec 18 2024
R-4.3-mac-aarch64NOTEDec 18 2024

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

Dependencies:abindAnnotationDbiaskpassassertthatbackportsbase64encBBmiscBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcacachemcallrcheckmatecliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestdplyreggevaluatefansifarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggrepelgluegridExtragtableheatmaplyhighrhmshtmltoolshtmlwidgetshttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpcaMethodspermutepheatmappillarpkgconfigplogrplotlyplyrpngprettyunitsprocessxprogresspromisesPRROCpspurrrqapR6rappdirsRColorBrewerRcppRcppArmadilloRCurlregistryreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesseriationsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexTSPtxdbmakerUCSC.utilsutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxml2XVectoryamlzlibbioc

OUTRIDER: OUTlier in RNA-seq fInDER

Rendered fromOUTRIDER.Rnwusingknitr::knitron Dec 18 2024.

Last update: 2024-04-26
Started: 2018-03-26

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
Estimation of QestimateBestQ
Filter expressionfilterExpression filterExpression,OutriderDataSet-method
Find the optimal encoding dimensionfindEncodingDim findEncodingDim, findInjectZscore
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