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 (3.9)

Identification of aberrent 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. Further OUTRIDER provides useful plotting function to analyze and visualize the results.

Author: Felix Brechtmann [aut, cre], Christian Mertes [aut, cre], Ange Matuseviciute [aut, cre], 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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("OUTRIDER", version = "3.9")

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
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Details

biocViews Alignment, GeneExpression, Genetics, RNASeq, Sequencing, Software, Transcriptomics
Version 1.1.0
License MIT + file LICENSE
Depends R (>= 3.4), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods
Imports BBmisc, Biobase, BiocGenerics, compiler, DESeq2(>= 1.16.1), GenomicRanges, ggplot2, ggpubr, gplots, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, Rcpp, reticulate, S4Vectors, scales, splines, stats, utils
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMySQL, AnnotationDbi, beeswarm, covr
SystemRequirements
Enhances
URL https://github.com/gagneurlab/OUTRIDER
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package OUTRIDER_1.1.0.tar.gz
Windows Binary OUTRIDER_1.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)
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 http://bioconductor.org/packages/OUTRIDER/
Package Downloads Report Download Stats

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