methylPipe

methylPipe and compEpiTools are complementary R/Bioconductor packages to streamline the integrative analysis of epigenomic datasets, including DNA methylation, histone marks, transcription factor binding, and other high-throughput data types. methylPipe specializes in analyzing DNA methylomes across various species, supporting high- to low-resolution data and accommodating different methylation contexts. It enables the analysis of whole-genome bisulfite sequencing experiments while allowing for the integration of targeted genomic data.

compEpiTools builds on the foundation laid by methylPipe, facilitating the integration of DNA methylation data with other epigenomic datasets. It offers tools for scoring epigenomic data within regions of interest, identifying enhancers, long non-coding RNAs, and RNA polymerase II dynamics. This package also provides comprehensive genomic region annotation, gene association with GeneOntology terms, and a flexible heatmap-based method for data integration.