bumphunter

bumphunter identifies differentially methylated regions (DMRs) and analyzes DNA methylation (DNAm) data generated by the Infinium HumanMethylation450 ('450k') array to characterize methylation changes across genomic loci.

Key Features:

• High-Throughput Analysis: Analyzes DNAm data at the scale of the Infinium HumanMethylation450 ('450k') array to evaluate methylation across ~450,000 loci.
• Statistical Techniques: Incorporates statistical methods to identify DMRs and assess their significance.
• Adaptability: Designed to accommodate data from the '450k' array and adapt to future DNAm measurement technologies.
• Comprehensive Methodology: Performs preprocessing of raw DNAm data, quality assessment, and detection of DMRs across kilobase to megabase genomic scales.
• Development Platform: Serves as a platform for development and testing of new analytical methods for DNAm data.
• Discovery Potential: Enables detection of methylation signals that can inform analyses previously reliant on sequencing-based techniques.

Scientific Applications:

• Epigenetics research: Enables genome-scale analysis of DNAm patterns for studies of epigenetic regulation.
• Gene regulation studies: Identifies DMRs that can be correlated with changes in gene expression and regulatory element activity.
• Disease mechanism investigations: Facilitates detection of methylation differences associated with disease states.
• Developmental biology: Allows characterization of methylation changes across developmental stages and tissues.

Methodology:

Preprocessing of raw DNAm data, quality assessment, and detection of differentially methylated regions (DMRs) across kilobase to megabase scales using statistical methods.