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Open Source Science

https://github.com/ay-lab/fithichip

Statistically Significant loops from HiChIP data

https://github.com/ay-lab/fithichip

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: nature.com
  • ○
    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.2%) to scientific vocabulary

Keywords

fithic hic-pro hichip
Last synced: 11 months ago · JSON representation

Repository

Statistically Significant loops from HiChIP data

Basic Info
  • Host: GitHub
  • Owner: ay-lab
  • License: mit
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 202 MB
Statistics
  • Stars: 32
  • Watchers: 6
  • Forks: 20
  • Open Issues: 19
  • Releases: 14
Topics
fithic hic-pro hichip
Created almost 9 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

FitHiChIP

Developers: Sourya Bhattacharyya, Ferhat Ay

La Jolla Institute for Immunology

La Jolla, CA 92037, USA

FitHiChIP analyzes HiChIP / PLAC-seq data and derives the statistical significant CIS interactions.

A comprehensive documentation of FitHiChIP is provided in

https://ay-lab.github.io/FitHiChIP/

Citation

FitHiChIP is now published at Nature Communications (https://www.nature.com/articles/s41467-019-11950-y)

If you are using FitHiChIP, please cite:

Sourya Bhattacharyya, Vivek Chandra, Pandurangan Vijayanand, and Ferhat Ay, Identification of significant chromatin contacts from HiChIP data by FitHiChIP, Nature Communications, Vol 10, No 4221, 2019, DOI: https://doi.org/10.1038/s41467-019-11950-y

Data repository

All the results in FitHiChIP, like the significant loops, HiChIP peak calling, performance analysis is now available in Zenodo

https://doi.org/10.5281/zenodo.3255048

Release notes - Version 11.0 (December 2022)

1. FitHiChIP now support HiChIP interactions in .hic and .cool / .mcool formats, in addition to the earlier formats.
2. Updated configuration files corresponding to these new input options.
3. Updated Docker and Singularity packages.
4. Differential HiChIP loop calling does not require ChIP-seq alignment files as a mandatory option. If users do not have any ChIP-seq alignment file, they can just proceed with the differential analysis without considering the difference in 1D.
5. FitHiChIP output loops are now converted to files compatible with WashU, UCSC and IGV epigenome browsers.

For the earlier release notes, please check the file Release_Notes.txt

Utility scripts for the manuscript

Check the folder *UtilScript* and corresponding README file for the links to various utility scripts used to generate the figures in this manuscript.

Contact

Please use the GitHub issues page for reporting any issues / suggestions (recommended).

Alternatively, you can e-mail us:

Owner

  • Login: ay-lab
  • Kind: user

GitHub Events

Total
  • Issues event: 2
  • Watch event: 2
  • Issue comment event: 2
Last Year
  • Issues event: 2
  • Watch event: 2
  • Issue comment event: 2

Dependencies

Dockerfile docker
  • r-base 4.1.0 build