OUTRIDER

DOI: 10.18129/B9.bioc.OUTRIDER  

OUTRIDER - OUTlier in RNA-Seq fInDER

Bioconductor version: Release (3.16)

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], Christian Mertes [aut, cre] , Agne Matuseviciute [aut], Michaela Fee Müller [ctb], Vicente Yepez [aut] , Julien Gagneur [aut]

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("OUTRIDER")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("OUTRIDER")

 

PDF	R Script	OUTRIDER: OUTlier in RNA-seq fInDER
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcriptomics
Version	1.16.3
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods
Imports	BBmisc, BiocGenerics, DESeq2(>= 1.16.1), generics, GenomicRanges, ggplot2, grDevices, heatmaply, pheatmap, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, reshape2, S4Vectors, scales, splines, stats, utils
LinkingTo	Rcpp, RcppArmadillo
Suggests	testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr
SystemRequirements
Enhances
URL	https://github.com/gagneurlab/OUTRIDER
Depends On Me
Imports Me	FRASER
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	OUTRIDER_1.16.3.tar.gz
Windows Binary	OUTRIDER_1.16.3.zip
macOS Binary (x86_64)	OUTRIDER_1.16.3.tgz
macOS Binary (arm64)	OUTRIDER_1.16.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/OUTRIDER
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OUTRIDER
Bioc Package Browser	https://code.bioconductor.org/browse/OUTRIDER/
Package Short Url	https://bioconductor.org/packages/OUTRIDER/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive