chromatin-state-inference

What problem does it solve?

ChromHMM-based chromatin state inference from histone modification ChIP-seq data to enable genome-wide state segmentation and annotation.

Core Features & Use Cases

• Chromatin state segmentation using ChromHMM across multiple histone marks.
• Model training and state annotation with user-specified genome assembly and bin size.
• Handles inputs as BED or BAM files and outputs to chromhmm_output with binarized and model directories.
• Prompts for missing inputs to ensure reproducibility.

Quick Start

Provide your BED or BAM files and the genome assembly, then run the chromHMM workflow to binarize data and train a state model.