Bioinformatics 101: DNA Methylation Analysis

Enrichment-Based Analysis Tools:

• 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