- MAT
- general purpose ChIP-chip peak calling algorithm
- CHARM
- primarily designed for enzyme digestion based analysis from the CHARM wet-lab protocol
- MEDME
- MeDIP analysis package
- BATMAN
- MeDIP analysis package
Bisulfite-Conversion Based Analysis Tools:
- RnBeads - R package for single-cell methylation data (currently in beta testing)
- IMA
- site and region based analysis for the Illumina methylation array
- COHCAP
- site and region based analysis for the Illumina methylation array as well as targeted BS-Seq
- CpGassoc
- site-based analysis for the Illumina methylation array
- MethLAB - MATLAB-based GUI
- NIMBL
- site-based analysis for the Illumina methylation array
- methylKit
- site and region-based analysis for BS-Seq data
- BSmooth
- BS-Seq alignment and analysis tool
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