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

RNA-seq analysis using multiple algorithms

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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

consensusDE HTML R Script
Reference Manual PDF


biocViews Clustering, MultipleComparison, Sequencing, Software, Transcriptomics
Version 1.23.0
In Bioconductor since BioC 3.8 (R-3.5) (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,, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils
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Follow Installation instructions to use this package in your R session.

Source Package consensusDE_1.23.0.tar.gz
Windows Binary
macOS Binary (x86_64) consensusDE_1.23.0.tgz
macOS Binary (arm64) consensusDE_1.23.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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