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This is the development version of CGEN; for the stable release version, see CGEN.

An R package for analysis of case-control studies in genetic epidemiology

Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("CGEN")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

CGEN Scan Vignette PDF R Script
CGEN Vignette PDF R Script
Reference Manual PDF


biocViews Clustering, MultipleComparison, SNP, Software
Version 3.39.0
In Bioconductor since BioC 2.7 (R-2.12) (13.5 years)
License GPL-2 + file LICENSE
Depends R (>= 4.0), survival, mvtnorm
Imports stats, graphics, utils, grDevices
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Source Package CGEN_3.39.0.tar.gz
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