OUTRIDER

DOI: 10.18129/B9.bioc.OUTRIDER  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see OUTRIDER.

OUTRIDER - OUTlier in RNA-Seq fInDER

Bioconductor version: 3.17

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>

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

Installation

To install this package, start R (version "4.3") 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 1.18.1
In Bioconductor since BioC 3.8 (R-3.5) (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_1.18.1.tar.gz
Windows Binary OUTRIDER_1.18.1.zip
macOS Binary (x86_64) OUTRIDER_1.18.1.tgz
macOS Binary (arm64) OUTRIDER_1.18.1.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: