This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see consensusDE.
Bioconductor version: 3.8
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 batch effects.
Author: Ashley J. Waardenberg
Maintainer: Ashley J. Waardenberg <a.waardenberg at gmail.com>
Citation (from within R,
enter citation("consensusDE")
):
To install this package, start R (version "3.5") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("consensusDE")
HTML | R Script | consensusDE |
Reference Manual | ||
Text | NEWS |
biocViews | Clustering, MultipleComparison, Software, Transcriptomics |
Version | 1.0.6 |
In Bioconductor since | BioC 3.8 (R-3.5) (0.5 years) |
License | GPL-3 |
Depends | R (>= 3.5), BiocGenerics |
Imports | limma, AnnotationDbi, Biobase, edgeR, BiocParallel, GenomicAlignments, EDASeq, RColorBrewer, GenomicFeatures, SummarizedExperiment, DESeq2(>= 1.20.0), pcaMethods, dendextend, RUVSeq, Rsamtools, S4Vectors, stats, TxDb.Dmelanogaster.UCSC.dm3.ensGene, airway, Biostrings |
LinkingTo | |
Suggests | knitr, rmarkdown |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | consensusDE_1.0.6.tar.gz |
Windows Binary | consensusDE_1.0.6.zip |
Mac OS X 10.11 (El Capitan) | consensusDE_1.0.6.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 | http://bioconductor.org/packages/consensusDE/ |
Package Downloads Report | Download Stats |
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