consensusDE

DOI: 10.18129/B9.bioc.consensusDE    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see consensusDE.

RNA-seq analysis using multiple algorithms

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

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

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")

 

HTML	R Script	consensusDE
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, MultipleComparison, Sequencing, Software, Transcriptomics
Version	1.6.0
In Bioconductor since	BioC 3.8 (R-3.5) (2 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
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	consensusDE_1.6.0.tar.gz
Windows Binary	consensusDE_1.6.0.zip
macOS 10.13 (High Sierra)	consensusDE_1.6.0.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	https://bioconductor.org/packages/consensusDE/
Package Downloads Report	Download Stats