DEGreport
This is the released version of DEGreport; for the devel version, see DEGreport.
Report of DEG analysis
Bioconductor version: Release (3.23)
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("DEGreport")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.48.0 |
| 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 |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DEGreport_1.48.0.tar.gz |
| Windows Binary (x86_64) | DEGreport_1.48.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | DEGreport_1.48.0.tgz |
| macOS Binary (sonoma-arm64) | DEGreport_1.48.0.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 |