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consensusDE
This is thereleased version of consensusDE; for the devel version, seeconsensusDE.
RNA-seq analysis using multiple algorithms
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("consensusDE")For older versions of R, please refer to the appropriateBioconductor 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 | 1.28.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 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
FollowInstallation instructions to use this package in your R session.
| Source Package | consensusDE_1.28.0.tar.gz |
| Windows Binary (x86_64) | consensusDE_1.28.0.zip |
| macOS Binary (x86_64) | consensusDE_1.28.0.tgz |
| macOS Binary (arm64) | consensusDE_1.28.0.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 |