methylKit

methylKit analyzes genome-wide cytosine methylation profiles from high-throughput bisulfite sequencing, including Reduced Representation Bisulfite Sequencing (RRBS) and its variants, target-capture methods, whole-genome bisulfite sequencing (WGBS), and base-pair resolution 5-hydroxymethylcytosine (5hmC) data from oxidative Bisulfite Sequencing (oxBS-Seq) and Tet-assisted Bisulfite Sequencing (TAB-Seq), to identify differential methylation and annotate genomic features.

Key Features:

• Data Handling and Compatibility: Supports input from SAM format files and requires Perl for reading SAM files, and explicitly handles data from RRBS, target-capture, WGBS, oxBS-Seq and TAB-Seq protocols.
• Clustering: Facilitates grouping of methylation patterns across samples to identify sample relationships.
• Sample Quality Visualization: Provides functions to assess and visualize data quality metrics for bisulfite sequencing experiments.
• Differential Methylation Analysis: Identifies statistically significant differences in methylation between sample groups at base or region level.
• Annotation Features: Links methylation changes to genomic features through automated annotation.
• Statistical Significance Determination: Performs determination of statistically significant bases or regions of DNA methylation.

Scientific Applications:

• Breast cancer epigenomics: Identification of regions of differential methylation and stratification of tumor subtypes in breast cancer datasets.
• Gene regulation and cellular specification: Detection of epigenetic modifications relevant to gene regulatory changes and cell-type specification.
• Disease mechanism studies: Characterization of epigenetic alterations implicated in disease mechanisms.

Methodology:

Reads SAM files (requires Perl) and applies clustering, sample quality visualization, differential methylation analysis, statistical significance testing, and annotation functions.