compEpiTools

compEpiTools performs integrative analysis and visualization of epigenomic datasets, including DNA methylomes, histone marks, transcription factor ChIP-seq, RNA-seq, and DNase-seq, to characterize chromatin state, transcriptional regulation, and DNA methylation contexts across genomic regions and samples.

Key Features:

• Integration of diverse epigenetic data types: Integrates high-resolution DNA methylomes with histone marks, transcription factor binding sites (ChIP-seq), RNA-seq, and DNase-seq, and supports whole-genome bisulfite sequencing and targeted methylation data across CpG and non-CpG contexts.
• Scoring and regional analysis: Provides methods to score epigenomic signals in regions of interest and to identify genomic features such as enhancers, long non-coding RNAs (lncRNAs), and RNA polymerase II stalling/elongation dynamics.
• Annotation and ontology association: Annotates genomic regions and associates genes with non-redundant Gene Ontology terms for downstream functional interpretation.
• Visualization and track integration: Produces flexible visualizations, including heatmaps, that combine annotation tracks with continuous or categorical data tracks to integrate multiple data types.

Scientific Applications:

• Gene regulation: Linking epigenetic marks and transcriptional output to investigate regulatory mechanisms of gene expression.
• Chromatin dynamics: Characterizing chromatin state changes and their relationships to transcription across samples and genomic regions.
• Functional implications of epigenetic modifications: Assessing how DNA methylation and histone modifications influence genomic function.
• Enhancer activity and non-coding RNA studies: Investigating enhancer activation, transcriptional regulation, and roles of long non-coding RNAs.

Methodology:

Integrates outputs from methylPipe with epigenomic datasets derived from high-throughput sequencing (whole-genome bisulfite sequencing, ChIP-seq, RNA-seq, DNase-seq) across multiple samples and genomic regions.