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✨
DESCRIPTION |NEWS
card.svg |card.png
OUTRIDER/json (API)

# 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)

immunooncology rnaseq transcriptomics alignment sequencing geneexpression genetics count-data diagnostics expression-analysis mendelian-genetics outlier-detection rna-seq openblas cpp

9.33 score 57 stars 1 packages 160 scripts 3 mentions 45 exports 162 dependencies

Last updated from:f5f7a6b9de. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	289
linux-devel-arm64	NOTE	471
linux-devel-x86_64	NOTE	572
source / vignettes	OK	597
linux-release-arm64	NOTE	494
linux-release-x86_64	NOTE	635
macos-release-arm64	NOTE	449
macos-release-x86_64	NOTE	752
macos-oldrel-arm64	NOTE	418
macos-oldrel-x86_64	NOTE	823
windows-devel	NOTE	676
windows-release	NOTE	692
windows-oldrel	NOTE	937
wasm-release	OK	303

Exports:aberrant computeGeneLength computeLatentSpace computePvalues computeZscores controlForConfounders counts counts<-dispersions estimateBestQ estimateSizeFactors filterExpression findInjectZscore fit fpkm fpm getBestQ makeExampleOutriderDataSet normalizationFactors normalizationFactors<-OUTRIDER OutriderDataSet padj plotAberrantPerSample plotCountCorHeatmap plotCountGeneSampleHeatmap plotDispEsts plotEncDimSearch plotExpectedVsObservedCounts plotExpressedGenes plotExpressionRank plotFPKM plotManhattan plotPowerAnalysis plotQQ plotSizeFactors plotVolcano pValue results sampleExclusionMask sampleExclusionMask<-sizeFactors sizeFactors<-theta zScore

Dependencies:abind AnnotationDbi askpass assertthat backports base64enc BBmisc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib ca cachem callr checkmate cigarillo cli cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray dendextend DESeq2 digest dplyr egg evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options gclus generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel glue gridExtra gtable heatmaply highr hms htmltools htmlwidgets httr httr2 IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl otel pcaMethods permute pheatmap pillar pkgconfig plotly plyr png pracma prettyunits processx progress promises PRROC ps purrr qap R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl registry reshape2 restfulr Rhtslib rjson rlang rmarkdown RMTstat Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seriation snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex TSP txdbmaker UCSC.utils utf8 vctrs vegan viridis viridisLite webshot withr xfun XML xml2 XVector yaml

OUTRIDER: OUTlier in RNA-seq fInDER

Rendered fromOUTRIDER.Rnwusingknitr::knitr

Last update: 2025-05-20
Started: 2018-03-26

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
Find the optimal encoding dimension	estimateBestQ estimateBestQ, findInjectZscore
Filter expression	filterExpression filterExpression,OutriderDataSet-method
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

Package: OUTRIDER 1.31.0

OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

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