OUTRIDER
This is the released version of OUTRIDER; for the devel version, see OUTRIDER.
OUTRIDER - OUTlier in RNA-Seq fInDER
Bioconductor version: Release (3.23)
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], Andrea Raithel [ctb], Vicente Yepez [aut]
, Julien Gagneur [aut]
Maintainer: Christian Mertes <mertes at in.tum.de>
citation("OUTRIDER")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| 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 | 1.30.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | file LICENSE |
| 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
Follow Installation instructions to use this package in your R session.
| Source Package | OUTRIDER_1.30.0.tar.gz |
| Windows Binary (x86_64) | OUTRIDER_1.30.0.zip |
| macOS Binary (big-sur-x86_64) | OUTRIDER_1.30.0.tgz |
| macOS Binary (sonoma-arm64) | OUTRIDER_1.30.0.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 |