consensusDE

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

RNA-seq analysis using multiple algorithms

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DOI: 10.18129/B9.bioc.consensusDE

Bioconductor version: Development (3.23)

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 "4.6") 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

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, MultipleComparison, Sequencing, Software, Transcriptomics

Version 1.29.0

In Bioconductor since BioC 3.8 (R-3.5) (7 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

System Requirements

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Package Archives

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

Source Package

Windows Binary (x86_64)

macOS Binary (x86_64)

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

Package Short Url https://bioconductor.org/packages/consensusDE/

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