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An R package that can efficiently perform the statistical analysis needed for increasingly large methylation datasets. CpGassoc can perform standard analyses of large datasets very quickly with no need to impute the data. It can handle mixed effects models with chip or batch entering the model as a random intercept. CpGassoc also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.

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CpGassoc classification

CpGassoc specifications

Software type:
Package
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
CpGassoc version 2.50
Requirements:
R (≥ 2.10), nlme

Publications

  • (Barfield et al., 2012) CpGassoc: an R function for analysis of DNA methylation microarray data. Bioinformatics.
    Published on: 2012 May 01
    PMID: 22451269

CpGassoc support

Maintainer

Credits

Institution(s)

Department of Bioinformatics and Biostatistics, School of Public Health, Emory University at Atlanta, GA, USA 30322

Link to literature

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