OUTRIDER

DOI: 10.18129/B9.bioc.OUTRIDER    

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

OUTRIDER - OUTlier in RNA-Seq fInDER

Bioconductor version: Development (3.15)

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 <brechtma at in.tum.de>, Christian Mertes <mertes at in.tum.de>, Agne Matuseviciute <yepez at in.tum.de>, Michaela Müller <gagneur at in.tum.de>, Fee Yepez <brechtma at in.tum.de>, Vicente Gagneur <mertes at in.tum.de>, Julien Brechtmann <yepez at in.tum.de>

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

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

Installation

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

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews Alignment, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcriptomics
Version 1.13.0
In Bioconductor since BioC 3.8 (R-3.5) (3 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, Rcpp, 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
Windows Binary
macOS 10.13 (High Sierra)
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

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