DEGreport
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see DEGreport.
Report of DEG analysis
Bioconductor version: 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("DEGreport")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, ReportWriting, Software, Visualization |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0) |
| 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 |
| 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_1.20.0.tar.gz |
| Windows Binary | DEGreport_1.20.0.zip |
| Mac OS X 10.11 (El Capitan) | DEGreport_1.20.0.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 3.9 | Source Archive |