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HiCPack is an Integrated package for Hi-C Data Analysis HiCPack is a high-level API, written in Python. It was developed with a focus on enabling fast experimentation. Being able to go from idea to result with the least possible delay is key to doing good research.

HiCPack is compatible with: Python 3.6-3.7.

Main Principles

HiCPack has some main principles:

  • User Friendly: HiCPack is an API designed for human beings, not machines. HiCPack offers consistent & simple APIs, it minimizes the number of user actions required for a common use case, and it provides clear feedback upon user error.

  • Modularity: A model is understood as a sequence or a graph of standalone modules that can be plugged together with as few restrictions as possible. In particular, embedding methods, semi-supervised algorithms schemes are all standalone modules that you can combine to create your own new model.

  • extensibility: It's very simple to add new modules, and existing modules provide examples. To be able to easily create new modules allows HiCPack suitable for advanced research.

  • Python Implementation: All models are described in Python code, which is compact, easier to debug, and allows for ease of extensibility.

Getting Started: HiCPack Usage

HiCPack --help
  usage : HiC-Pack -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v]
  Use option -h|--help for more information

  HiC-Pack 1.0.10

   -i|--input INPUT : input data folder; Must contains a folder per sample with input files
   -o|--output OUTPUT : output folder
   -c|--conf CONFIG : configuration file for Hi-C processing
   [-p|--parallel] : if specified run HiC-Pro on a cluster
   [-s|--step ANALYSIS_STEP] : run only a subset of the HiC-Pro workflow; if not specified the complete workflow is run
      mapping: perform reads alignment
      proc_hic: perform Hi-C filtering
      quality_checks: run Hi-C quality control plots
      build_contact_maps: build raw inter/intrachromosomal contact maps
      bg_model: Applies a specific background model to raw contact maps
      visualization: Provide some visualizations for contact maps
      tadcalling: Runs a specific TAD Calling algorithm on significant interactions
   [-h|--help]: help
   [-v|--version]: version


Please feel free to ask questions:

You can also post bug reports and feature requests in GitHub issues. Please Make sure to read our guidelines first.