DOI: 10.18129/B9.bioc.OUTRIDER    


Bioconductor version: Release (3.8)

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.

Author: Felix Brechtmann [aut, cre], Christian Mertes [aut, cre], Ange Matuseviciute [aut, cre], Vicente Yepez [aut], Julien Gagneur [aut]

Maintainer: Christian Mertes <mertes at in.tum.de>

Citation (from within R, enter citation("OUTRIDER")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("OUTRIDER", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.


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PDF R Script OUTRIDER: OUTlier in RNA-seq fInDER
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biocViews Alignment, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcriptomics
Version 1.0.4
In Bioconductor since BioC 3.8 (R-3.5) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.5), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods
Imports BBmisc, Biobase, BiocGenerics, compiler, DESeq2(>= 1.16.1), GenomicRanges, ggplot2, ggpubr, gplots, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, Rcpp, reticulate, S4Vectors, scales, splines, stats, utils
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMySQL, AnnotationDbi, beeswarm, covr
URL https://github.com/gagneurlab/OUTRIDER
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Source Package OUTRIDER_1.0.4.tar.gz
Windows Binary OUTRIDER_1.0.4.zip
Mac OS X 10.11 (El Capitan) OUTRIDER_1.0.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/OUTRIDER
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/OUTRIDER
Package Short Url http://bioconductor.org/packages/OUTRIDER/
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