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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/OUTRIDER.html below:

Bioconductor - OUTRIDER (development version)

OUTRIDER

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

OUTRIDER - OUTlier in RNA-Seq fInDER

Bioconductor version: Development (3.22)

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

To install this package, start R (version "4.5") and enter:


if (!require("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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("OUTRIDER")
Details biocViews Alignment, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcriptomics Version 1.27.1 In Bioconductor since BioC 3.8 (R-3.5) (6.5 years) License file LICENSE Depends R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods Imports BBmisc, BiocGenerics, 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, denoiseR 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.

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