OUTRIDER
This is thereleased version of OUTRIDER; for the devel version, seeOUTRIDER.
OUTRIDER - OUTlier in RNA-Seq fInDER
Bioconductor version: Release (3.22)
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("OUTRIDER")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("OUTRIDER")For older versions of R, please refer to the appropriateBioconductor 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 | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment,GeneExpression,Genetics,ImmunoOncology,RNASeq,Sequencing,Software,Transcriptomics |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| License | fileLICENSE |
| 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 |
See More
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | OUTRIDER_1.28.0.tar.gz |
| Windows Binary (x86_64) | OUTRIDER_1.28.0.zip (64-bit only) |
| macOS Binary (x86_64) | OUTRIDER_1.28.0.tgz |
| macOS Binary (arm64) | OUTRIDER_1.28.0.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 |