OUTRIDER
OUTRIDER - OUTlier in RNA-Seq fInDER
Bioconductor version: 3.24 · Package version: 1.31.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("OUTRIDER")Details
| Maintainer | Christian Mertes <mertes@in.tum.de> |
| Author | Felix Brechtmann [aut] (ORCID: <https://orcid.org/0000-0002-0110-152X>), Christian Mertes [aut, cre] (ORCID: <https://orcid.org/0000-0002-1091-205X>), Agne Matuseviciute [aut], Michaela Fee Müller [ctb], Andrea Raithel [ctb], Vicente Yepez [aut] (ORCID: <https://orcid.org/0000-0001-7916-3643>), Julien Gagneur [aut] (ORCID: <https://orcid.org/0000-0002-8924-8365>) |
| License | file LICENSE |
| URL | https://github.com/gagneurlab/OUTRIDER |
| Bug Reports | https://github.com/gagneurlab/OUTRIDER/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/OUTRIDER/ |
Citation
From within R, enter citation("OUTRIDER"):
Felix Brechtmann, Christian Mertes, Agne Matuseviciute, Vicente Yepez, Julien Gagneur. OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER. doi:10.18129/B9.bioc.OUTRIDER, R package version 1.31.0, https://bioconductor.org/packages/OUTRIDER.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | OUTRIDER_1.31.0.tar.gz |
| Windows binary (x86_64) | OUTRIDER_1.31.0.zip |
| macOS binary (arm64) | OUTRIDER_1.31.0.tgz |
| macOS binary (x86_64) | OUTRIDER_1.31.0.tgz |
Dependencies
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
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase
Reverse dependencies
Imports Me (1): FRASER