EGAD
This is the development version of EGAD; for the stable release version, see EGAD.
Extending guilt by association by degree
Bioconductor version: Development (3.24)
The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.
Author: Sara Ballouz [aut, cre], Melanie Weber [aut, ctb], Paul Pavlidis [aut], Jesse Gillis [aut, ctb]
Maintainer: Sara Ballouz <sarahballouz at gmail.com>
citation("EGAD")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("EGAD")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | FunctionalGenomics, FunctionalPrediction, GenePrediction, GraphAndNetwork, Network, NetworkEnrichment, Software, SystemsBiology |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.5) |
| Imports | gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo, igraph, plyr, MASS, RCurl, methods |
| System Requirements | |
| URL |
See More
| Suggests | knitr, testthat, rmarkdown, markdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EGAD_1.41.0.tar.gz |
| Windows Binary (x86_64) | EGAD_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | EGAD_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | EGAD_1.41.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/EGAD |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/EGAD |
| Bioc Package Browser | https://code.bioconductor.org/browse/EGAD/ |
| Package Short Url | https://bioconductor.org/packages/EGAD/ |
| Package Downloads Report | Download Stats |