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MethLAB

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Performs analyses of array-based DNA methylation data. MethLAB is a graphical user interface (GUI) package. For each cytosine–phosphate–guanine (CpG) site, the software models methylation as a function of a categorical or continuous phenotype and other covariates. This package can incorporate both continuous and categorical covariates, as well as fixed or random batch or chip effects. It has been designed to optimize memory use during analyses.

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MethLAB classification

MethLAB specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
TXT or CSV
Operating system:
Unix/Linux
Computer skills:
Medium
Stability:
Stable
Interface:
Command line interface, Graphical user interface
Input data:
The phenotype file, the methylation file, and the annotation file.
Output data:
A text file that contains the t-statistics, p-values and flags indicating the Bonferroni/Holm significance and FDR significance of each CpG site for a given model, Q-Q Plots, Manhattan Plot, plots of individual CpG sites and a log file.
Programming languages:
R
Version:
2.0
Maintained:
Yes

MethLAB distribution

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No versioning.

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MethLAB support

Documentation

Maintainers

  • Karen N. Conneely <>
  • Varun Kilaru <>

Credits

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Publications

Institution(s)

Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA; Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA; Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA; Department of Human Genetics, Emory University, Atlanta, GA, USA

Funding source(s)

Supported in part by the National Institute of Mental Health (MH088609 and MH085806).

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