CGEN
This is the released version of CGEN; for the devel version, see CGEN.
An R package for analysis of case-control studies in genetic epidemiology
Bioconductor version: Release (3.23)
This is a package for analysis of case-control data in genetic epidemiology. It provides a set of statistical methods for evaluating gene-environment (or gene-genes) interactions under multiplicative and additive risk models, with or without assuming gene-environment (or gene-gene) independence in the underlying population.
Author: Samsiddhi Bhattacharjee [aut], Nilanjan Chatterjee [aut], Summer Han [aut], Minsun Song [aut], William Wheeler [aut], Matthieu de Rochemonteix [aut], Nilotpal Sanyal [aut], Justin Lee [cre]
Maintainer: Justin Lee <jhylee at stanford.edu>
citation("CGEN")):
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("CGEN")
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("CGEN")| CGEN Scan Vignette | R Script | |
| CGEN Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, MultipleComparison, SNP, Software |
| Version | 3.48.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (16 years) |
| License | GPL-2 + file LICENSE |
| Depends | R (>= 4.0), survival, mvtnorm |
| Imports | stats, graphics, utils, grDevices |
| System Requirements | |
| URL |
See More
| Suggests | cluster |
| 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 | CGEN_3.48.0.tar.gz |
| Windows Binary (x86_64) | CGEN_3.48.0.zip |
| macOS Binary (big-sur-x86_64) | CGEN_3.48.0.tgz |
| macOS Binary (sonoma-arm64) | CGEN_3.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CGEN |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CGEN |
| Bioc Package Browser | https://code.bioconductor.org/browse/CGEN/ |
| Package Short Url | https://bioconductor.org/packages/CGEN/ |
| Package Downloads Report | Download Stats |