DMRichR

DMRichR analyzes differentially methylated regions (DMRs) for epigenetic research, with particular utility for non-model organisms.

Key Features:

• DMR detection: Leverages existing algorithms including dmrseq and bsseq for differentially methylated region identification.
• Data processing: Provides tools for processing DNA methylation data.
• Annotation: Includes functionality for annotating DMRs.
• Visualization: Provides tools for visualizing DNA methylation analysis results.
• Non-model organism support: Adaptable for custom, non-model genomes through modification of code and computation of species-specific BSgenome, TxDb, org.db packages, and CpG islands tracks using the makeCGI package.

Scientific Applications:

• Epigenetic research: Supports analysis of DNA methylation patterns in epigenetic studies.
• Ecological and environmental research: Enables epigenetic analysis in environmentally relevant non-model species such as Daphnia for ecological risk assessment of chemicals causing aberrant methylation patterns.
• Evolutionary biology: Facilitates epigenetic studies in evolutionary model organisms with limited existing tool support.

Methodology:

DMRichR leverages the dmrseq and bsseq algorithms. For non-model genome adaptation, the workflow involves modification of specific code, computation of species-specific BSgenome, TxDb, and org.db packages, and computation of a CpG islands track using the makeCGI package.