consensusDE

DOI: 10.18129/B9.bioc.consensusDE    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see consensusDE.

RNA-seq analysis using multiple algorithms

Bioconductor version: 3.9

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

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

Installation

To install this package, start R (version "3.6") 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	1.2.1
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
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
Links To Me
Build Report

Package Archives

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

Source Package	consensusDE_1.2.1.tar.gz
Windows Binary	consensusDE_1.2.1.zip
Mac OS X 10.11 (El Capitan)	consensusDE_1.2.1.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