DEGreport

This is the development version of DEGreport; for the stable release version, see DEGreport.

Report of DEG analysis

Bioconductor version: Development (3.19)

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], Ivo Zeller [ctb]

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

Citation (from within R, enter citation("DEGreport")):

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("DEGreport")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, ReportWriting, Software, Visualization
Version	1.39.4
In Bioconductor since	BioC 3.0 (R-3.1) (9.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0.0)
Imports	utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, stringi, S4Vectors, SummarizedExperiment, tidyr, tibble
System Requirements
URL	http://lpantano.github.io/DEGreport/
Bug Reports	https://github.com/lpantano/DEGreport/issues

Suggests	BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat
Linking To
Enhances
Depends On Me
Imports Me	isomiRs
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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	https://bioconductor.org/packages/DEGreport/
Package Downloads Report	Download Stats