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consensusDE

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

RNA-seq analysis using multiple algorithms


Bioconductor version: Development (3.19)

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 "4.4") 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 1.21.0
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, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils
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Package Archives

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

Source Package consensusDE_1.21.0.tar.gz
Windows Binary consensusDE_1.21.0.zip
macOS Binary (x86_64) consensusDE_1.21.0.tgz
macOS Binary (arm64) consensusDE_1.21.0.tgz
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