DEGreport

DOI: 10.18129/B9.bioc.DEGreport    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see DEGreport.

Report of DEG analysis

Bioconductor version: 3.8

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], Radhika Khetani [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 (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DEGreport")

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("DEGreport")

 

HTML	R Script	QC and downstream analysis for differential expression RNA-seq
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, ReportWriting, Software, Visualization
Version	1.18.1
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.4.0)
Imports	utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, lasso2, magrittr, Nozzle.R1, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr, tibble
LinkingTo
Suggests	BiocStyle, AnnotationDbi, limma, pheatmap, knitr, rmarkdown, statmod, testthat
SystemRequirements
Enhances
URL	http://lpantano.github.io/DEGreport/
BugReports	https://github.com/lpantano/DEGreport/issues
Depends On Me
Imports Me	isomiRs
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	DEGreport_1.18.1.tar.gz
Windows Binary	DEGreport_1.18.1.zip
Mac OS X 10.11 (El Capitan)	DEGreport_1.18.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DEGreport
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DEGreport
Package Short Url	http://bioconductor.org/packages/DEGreport/
Package Downloads Report	Download Stats