OUTRIDER

This is the development version of OUTRIDER; for the stable release version, see OUTRIDER.

OUTRIDER - OUTlier in RNA-Seq fInDER

Bioconductor version: Development (3.21)

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] (ORCID: ), 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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcriptomics
Version	1.25.0
In Bioconductor since	BioC 3.8 (R-3.5) (6 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, ggrepel, grDevices, heatmaply, pheatmap, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, reshape2, 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

Package Archives

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

Source Package	OUTRIDER_1.25.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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