methylPipe

methylPipe processes and analyzes DNA methylation data across CpG and non-CpG contexts, supporting base- and low-resolution methylomes including (hydroxy-)methyl-cytosines from whole-genome bisulfite sequencing and targeted genomic data.

Key Features:

• Memory Efficiency: Optimized for memory-efficient processing of large-scale DNA methylation datasets.
• Multiple WGBS and targeted data support: Supports multiple whole-genome bisulfite sequencing experiments and compatibility with targeted genomic data.
• Resolution flexibility: Integrates base-resolution and low-resolution methylation data.
• CpG and non-CpG contexts: Analyzes (hydroxy-)methyl-cytosines in both CpG and non-CpG sequence contexts.
• Versatile data integration: Integrates DNA methylation data derived from diverse methodologies.

Scientific Applications:

• Epigenomic data integration: Integrates DNA methylation data with other epigenomics datasets such as RNA-seq, ChIP-seq, and DNase-seq and interoperates with compEpiTools.
• Enhancer and lncRNA identification: Facilitates identification of enhancers, long non-coding RNAs (lncRNAs), and RNA polymerase II stalling/elongation dynamics.
• Gene Ontology annotation: Annotates genomic regions and associates corresponding genes with non-redundant GeneOntology terms.

Methodology:

Provides a streamlined workflow for processing and analyzing DNA methylation data. Includes flexible heatmap-based methods to integrate different data types by combining annotation tracks with continuous or categorical data tracks.