DEGreport

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

Report of DEG analysis

Bioconductor version: Development (3.24)

Creation of ready-to-share figures 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")):

Lorena Pantano. DEGreport: Report of DEG analysis. doi:10.18129/B9.bioc.DEGreport, R package version 1.49.0, https://bioconductor.org/packages/DEGreport.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, ReportWriting, Software, Visualization
Version	1.49.0
In Bioconductor since	BioC 3.0 (R-3.1) (12 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	carnation
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DEGreport_1.49.0.tar.gz
Windows Binary (x86_64)	DEGreport_1.49.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	DEGreport_1.49.0.tgz
macOS Binary (sonoma-arm64)	DEGreport_1.49.0.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	https://bioconductor.org/packages/DEGreport/
Package Downloads Report	Download Stats