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This article is part of a special issue on epigenomics.

Open Access Highly Accessed Software

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Altuna Akalin12*, Matthias Kormaksson3, Sheng Li12, Francine E Garrett-Bakelman4, Maria E Figueroa5, Ari Melnick46 and Christopher E Mason12*

Author Affiliations

1 Department of Physiology and Biophysics, 1305 York Ave., Weill Cornell Medical College, New York, NY 10065, USA

2 The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 1305 York Ave., Weill Cornell Medical College, New York, NY 10065, USA

3 Department of Public Health, Weill Cornell Medical College, 1300 York Ave., New York, NY 10065, USA

4 Department of Medicine, Division of Hematology/Oncology, 1300 York Ave., Weill Cornell Medical College, New York, NY 10065, USA

5 Department of Pathology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA

6 Department of Pharmacology, 1300 York Ave., Weill Cornell Medical College, New York, NY 10065, USA

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Genome Biology 2012, 13:R87  doi:10.1186/gb-2012-13-10-r87

Published: 3 October 2012

Additional files

Additional file 1:

methylKit v0.5.3. This version of methylKit is included for archival purposes only. Please download the most recent version from [16].

Format: GZ Size: 1.1MB Download file

Open Data

Additional file 2:

methylKit User Guide. A vignette file to accompany the methylKit software package; the most recent software and vignette can be downloaded at [16].

Format: PDF Size: 677KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

methylKit documentation. Documentation for functions and classes in the methylKit software package; the most recent software and documentation can be downloaded at [16].

Format: PDF Size: 131KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

R script for example analysis. The file contains R commands that are needed to do analysis and to produce graphs used in this manuscript. The file contains both the commands and detailed comments on how those commands can be used. An up to date version of this script will be consistently maintained at [16].

Format: R Size: 5KB Download file

Open Data