Processing Multi-Epigenomics Data

This is a comprehensive toolkit for analyzing epigenomic data including ChIP-seq and CUT&Tag experiments.

To install the packages, please follow the instructions in our install page

multiEpiPrep is a command-line tool for preprocessing raw sequencing data. It includes functions for alignment, quality control, signal track generation, and fragment-level analysis. The tool is designed to be fast, reproducible, and independent of R, utilizing bowtie2 for alignment and Picard for duplicate removal.

multiEpiCore is a comprehensive R package designed for downstream analysis. It provides functions for count matrix processing, quality control, clustering analysis, differential region identification, motif enrichment, fragment decomposition, and advanced visualization including heatmaps and scatter plots.