Welcome to the Open Chromosome Collective!
We are a group of computational biologists working on chromosome structure and interested in developing open source tools for the wider community.
We are particularly interested in the 3D organization of chromosomes, and most of the tools are focused on the analysis of data obtained using Hi-C and related technologies. We like our tools to be easy to use, flexible, to facilitate active development of novel analytical approaches, and scalable, to make use of the latest and largest datasets.
For analysis of Hi-C (and related) data, we have a suite of tools:
- pairtools for analysis and filtering of mapped reads
- cooler for generation, normalization and storage of interaction matrices
- distiller - a Nextflow pipeline for automation of Hi-C data processing, from reads to Cooler files
- cooltools for extracting and quantifying features from Hi-C data, including: contacts vs. distance, compartments and saddles, insulation, and peaks
- coolpup.py for flexible pileup analysis
- quaich - a Snakemake pipeline for automated Hi-C postprocessing using cooltools and coolpup.py
- bioframe provides a framework for genomic data analysis using Pandas DataFrames, including genomic interval arithmetic
- polychrom simplifies polymer simulations for in silico experiments with chromosomes
Please interact with us on GitHub (we are open!), or join our Slack for more interactive discussions.