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DEGreport

Report of DEG analysis


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
QC and downstream analysis for differential expression RNA-seq HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, ReportWriting, Software, Visualization
Version 1.38.5
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
See More
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 DEGreport_1.38.5.tar.gz
Windows Binary DEGreport_1.38.5.zip (64-bit only)
macOS Binary (x86_64) DEGreport_1.38.5.tgz
macOS Binary (arm64) DEGreport_1.38.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/DEGreport
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DEGreport
Bioc Package Browser https://code.bioconductor.org/browse/DEGreport/
Package Short Url https://bioconductor.org/packages/DEGreport/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive