This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

consensusDE

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

RNA-seq analysis using multiple algorithms

Bioconductor version: Development (3.18)

This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove unwanted sources of variation.

Author: Ashley J. Waardenberg [aut, cre], Martha M. Cooper [ctb]

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

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("consensusDE")

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")
consensusDE HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, MultipleComparison, Sequencing, Software, Transcriptomics
Version 1.19.0
In Bioconductor since BioC 3.8 (R-3.5) (5 years)
License GPL-3
Depends R (>= 3.5), BiocGenerics
Imports airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2(>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils
Linking To
Suggests knitr, rmarkdown
System Requirements
Enhances
URL
See More
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_1.19.0.tar.gz
Windows Binary consensusDE_1.19.0.zip
macOS Binary (x86_64) consensusDE_1.19.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/consensusDE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/consensusDE
Bioc Package Browser https://code.bioconductor.org/browse/consensusDE/
Package Short Url https://bioconductor.org/packages/consensusDE/
Package Downloads Report Download Stats