DEGreport

DOI: 10.18129/B9.bioc.DEGreport    

Report of DEG analysis

Bioconductor version: Release (3.6)

Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

Author: Lorena Pantano [aut, cre], John Hutchinson [ctb], Victor Barrera [ctb], Mary Piper [ctb], Kenneth Daily [ctb], Thanneer Malai Perumal [ctb], Rory Kirchner [ctb], Michael Steinbaugh [ctb]

Maintainer: Lorena Pantano <lorena.pantano at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DEGreport")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DEGreport")

 

PDF	R Script	DEGreport
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, RNASeq, ReportWriting, Software, Visualization
Version	1.14.1
In Bioconductor since	BioC 3.0 (R-3.1) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.4.0), quantreg
Imports	utils, methods, Biobase, BiocGenerics, ConsensusClusterPlus, S4Vectors, SummarizedExperiment, DESeq2, ggplot2, cowplot, ggrepel, Nozzle.R1, edgeR, cluster, logging, dplyr, tidyr, tibble, reshape, ComplexHeatmap, knitr, grDevices, magrittr, scales, stats, psych, rlang
LinkingTo
Suggests	BiocStyle, AnnotationDbi, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DEGreport_1.14.1.tar.gz
Windows Binary	DEGreport_1.14.1.zip
Mac OS X 10.11 (El Capitan)	DEGreport_1.14.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DEGreport
Package Short Url	http://bioconductor.org/packages/DEGreport/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive