consensusDE

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see consensusDE.

RNA-seq analysis using multiple algorithms


Bioconductor version: 3.10

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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")
consensusDE HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, MultipleComparison, Sequencing, Software, Transcriptomics
Version 1.4.0
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
System Requirements
URL
See More
Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package consensusDE_1.4.0.tar.gz
Windows Binary consensusDE_1.4.0.zip
Mac OS X 10.11 (El Capitan) consensusDE_1.4.0.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
Old Source Packages for BioC 3.10 Source Archive