DEGreport

DOI: 10.18129/B9.bioc.DEGreport    

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

Report of DEG analysis

Bioconductor version: Development (3.9)

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DEGreport", version = "3.9")

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, RNASeq, ReportWriting, Software, Visualization
Version 1.19.0
In Bioconductor since BioC 3.0 (R-3.1) (4 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_1.19.0.tar.gz
Windows Binary DEGreport_1.19.0.zip
Mac OS X 10.11 (El Capitan) DEGreport_1.19.0.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 http://bioconductor.org/packages/DEGreport/
Package Downloads Report Download Stats

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