consensusDE

DOI: 10.18129/B9.bioc.consensusDE    

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

RNA-seq analysis using multiple algorithms

Bioconductor version: Development (3.9)

This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq", but can be easily extended. It uses RUV-seq (optional) to remove batch effects.

Author: Ashley J. Waardenberg

Maintainer: Ashley J. Waardenberg <a.waardenberg at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("consensusDE", version = "3.9")

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("consensusDE")

 

HTML R Script consensusDE
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, MultipleComparison, Software, Transcriptomics
Version 1.1.0
License GPL-3
Depends R (>= 3.5)
Imports limma, AnnotationDbi, Biobase, edgeR, BiocParallel, GenomicAlignments, EDASeq, RColorBrewer, GenomicFeatures, SummarizedExperiment, DESeq2(>= 1.20.0), pcaMethods, dendextend, RUVSeq, Rsamtools, S4Vectors, stats, TxDb.Dmelanogaster.UCSC.dm3.ensGene, airway, Biostrings
LinkingTo
Suggests knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package consensusDE_1.1.0.tar.gz
Windows Binary consensusDE_1.1.0.zip
Mac OS X 10.11 (El Capitan) consensusDE_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/consensusDE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/consensusDE
Package Short Url http://bioconductor.org/packages/consensusDE/
Package Downloads Report Download Stats

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