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>
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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, MultipleComparison, Sequencing, Software, Transcriptomics |
| Version | 1.2.1 |
| 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_1.2.1.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 |
| 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 3.9 | Source Archive |