consensusDE
This is the development version of consensusDE; for the stable release version, see consensusDE.
RNA-seq analysis using multiple algorithms
Bioconductor version: Development (3.20)
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>
citation("consensusDE")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
NEWS | Text |
Details
biocViews | Clustering, MultipleComparison, Sequencing, Software, Transcriptomics |
Version | 1.23.0 |
In Bioconductor since | BioC 3.8 (R-3.5) (6 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_1.23.0.tar.gz |
Windows Binary | consensusDE_1.23.0.zip |
macOS Binary (x86_64) | consensusDE_1.23.0.tgz |
macOS Binary (arm64) | consensusDE_1.23.0.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 |