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

Need some help? Ask on the Bioconductor Support site!

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

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Suggests knitr, rmarkdown

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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