DOI: 10.18129/B9.bioc.OUTRIDER    

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


Bioconductor version: Development (3.15)

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 <brechtma at in.tum.de>, Christian Mertes <mertes at in.tum.de>, Agne Matuseviciute <yepez at in.tum.de>, Michaela Müller <gagneur at in.tum.de>, Fee Yepez <brechtma at in.tum.de>, Vicente Gagneur <mertes at in.tum.de>, Julien Brechtmann <yepez at in.tum.de>

Maintainer: Christian Mertes <mertes at in.tum.de>

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


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biocViews Alignment, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcriptomics
Version 1.13.0
In Bioconductor since BioC 3.8 (R-3.5) (3 years)
License MIT + file LICENSE
Depends R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods
Imports BBmisc, BiocGenerics, DESeq2(>= 1.16.1), generics, GenomicRanges, ggplot2, grDevices, heatmaply, pheatmap, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, Rcpp, reshape2, S4Vectors, scales, splines, stats, utils
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr
URL https://github.com/gagneurlab/OUTRIDER
Depends On Me
Imports Me FRASER
Suggests Me
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