OUTRIDER

This is the released version of OUTRIDER; for the devel version, see OUTRIDER.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8

OUTRIDER - OUTlier in RNA-Seq fInDER

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-0110-152X , Christian Mertes [aut, cre] ORCID: 0000-0002-1091-205X , Agne Matuseviciute [aut], Michaela Fee Müller [ctb], Andrea Raithel [ctb], Vicente Yepez [aut] ORCID: 0000-0001-7916-3643 , Julien Gagneur [aut] ORCID: 0000-0002-8924-8365

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

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

Felix Brechtmann, Christian Mertes, Agne Matuseviciute, Vicente Yepez, Julien Gagneur. OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER. doi:10.18129/B9.bioc.OUTRIDER, R package version 1.30.0, https://bioconductor.org/packages/OUTRIDER.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcriptomics
Version	1.30.0
In Bioconductor since	BioC 3.8 (R-3.5) (8 years)
License	file LICENSE
Depends	R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, methods
Imports	BBmisc, BiocGenerics, data.table, DESeq2 (>= 1.16.1), generics, GenomicRanges, ggplot2, ggrepel, graphics, grDevices, heatmaply, IRanges, matrixStats, pcaMethods, pheatmap, plotly, plyr, pracma, PRROC, RColorBrewer, reshape2, RMTstat, S4Vectors, scales, splines, stats, txdbmaker, utils
System Requirements
URL	https://github.com/gagneurlab/OUTRIDER
Bug Reports	https://github.com/gagneurlab/OUTRIDER/issues

Suggests	testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase
Linking To	Rcpp, RcppArmadillo
Enhances
Depends On Me
Imports Me	FRASER
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	OUTRIDER_1.30.0.tar.gz
Windows Binary (x86_64)	OUTRIDER_1.30.0.zip
macOS Binary (big-sur-x86_64)	OUTRIDER_1.30.0.tgz
macOS Binary (sonoma-arm64)	OUTRIDER_1.30.0.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	https://bioconductor.org/packages/OUTRIDER/
Package Downloads Report	Download Stats