Package: OUTRIDER 1.23.0
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:
OUTRIDER_1.23.0.tar.gz
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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')) |
Bug tracker:https://github.com/gagneurlab/outrider/issues
On BioConductor:OUTRIDER-1.23.0(bioc 3.20)OUTRIDER-1.22.0(bioc 3.19)
Last updated 2 months agofrom:87c9a4454c
Exports:aberrantcomputeGeneLengthcomputeLatentSpacecomputePvaluescomputeZscorescontrolForConfounderscountscounts<-dispersionsestimateBestQestimateSizeFactorsfilterExpressionfindEncodingDimfindInjectZscorefitfpkmfpmgetBestQmakeExampleOutriderDataSetnormalizationFactorsnormalizationFactors<-OUTRIDEROutriderDataSetpadjplotAberrantPerSampleplotCountCorHeatmapplotCountGeneSampleHeatmapplotDispEstsplotEncDimSearchplotExpectedVsObservedCountsplotExpressedGenesplotExpressionRankplotFPKMplotManhattanplotPowerAnalysisplotQQplotSizeFactorsplotVolcanopValueresultssampleExclusionMasksampleExclusionMask<-sizeFactorssizeFactors<-thetazScore
Dependencies:abindAnnotationDbiaskpassassertthatbackportsbase64encBBmiscBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcacachemcallrcheckmatecliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestdplyreggevaluatefansifarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggrepelgluegridExtragtableheatmaplyhighrhmshtmltoolshtmlwidgetshttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpcaMethodspermutepheatmappillarpkgconfigplogrplotlyplyrpngprettyunitsprocessxprogresspromisesPRROCpspurrrqapR6rappdirsRColorBrewerRcppRcppArmadilloRCurlregistryreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesseriationsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexTSPtxdbmakerUCSC.utilsutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Number of aberrant events | aberrant aberrant,OutriderDataSet-method |
| Extracting the gene length from annotations | computeGeneLength |
| Extracting the latent space | computeLatentSpace |
| Calculate P-values | computePvalues computePvalues,OutriderDataSet-method |
| Z score computation | computeZscores 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 Q | estimateBestQ |
| Filter expression | filterExpression filterExpression,OutriderDataSet-method |
| Find the optimal encoding dimension | findEncodingDim findEncodingDim, findInjectZscore |
| Fit the negative binomial distribution | fit fit.OutriderDataSet |
| Calculate FPM and FPKM values | fpkm fpm |
| Getter/Setter functions | dispersion, dispersions dispersions,OutriderDataSet-method getBestQ getter_setter_functions padj padj, pValue pValue, theta theta, zScore zScore, |
| Create example data sets for OUTRIDER | makeExampleOutriderDataSet |
| 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 events | OUTRIDER |
| OutriderDataSet class and constructors | OutriderDataSet OutriderDataSet-class |
| Visualization functions for OUTRIDER | plotAberrantPerSample 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 exclusion | sampleExclusionMask sampleExclusionMask, sampleExclusionMask<- `sampleExclusionMask<-` |
| SizeFactors accessor and estimation function | estimateSizeFactors estimateSizeFactors,OutriderDataSet-method sizeFactors sizeFactors,OutriderDataSet-method sizeFactors<- sizeFactors<-,OutriderDataSet,NULL-method sizeFactors<-,OutriderDataSet,numeric-method |
