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Bioconductor - DEGreport

DEGreport

This is the released version of DEGreport; for the devel version, see DEGreport.

Report of DEG analysis

Bioconductor version: Release (3.21)

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")): Installation

To install this package, start R (version "4.5") 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 1.44.0 In Bioconductor since BioC 3.0 (R-3.1) (10.5 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 Package Archives

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

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