stripepy-hic

StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning

https://github.com/paulsengroup/stripepy

Science Score: 67.0%

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CITATION.cff file
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Low similarity (14.3%) to scientific vocabulary

Keywords

architectural-stripes bioinformatics cli-application hi-c loop-extrusion python

Last synced: 4 months ago · JSON representation ·

Repository

StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning

Basic Info

Host: GitHub
Owner: paulsengroup
License: mit
Language: Python
Default Branch: main
Homepage: https://stripepy.readthedocs.io
Size: 2.71 MB

Statistics

Stars: 8
Watchers: 4
Forks: 3
Open Issues: 5
Releases: 5

Topics

architectural-stripes bioinformatics cli-application hi-c loop-extrusion python

Created over 1 year ago · Last pushed 5 months ago

Metadata Files

Readme Citation

StripePy

Paper
Downloads
Documentation
CI
License

StripePy is a CLI application written in Python that recognizes architectural stripes found in the interaction matrix files generated by Chromosome Conformation Capture experiments, such as Hi-C and Micro-C.

StripePy is developed on Linux and macOS and is also tested on Windows. Installing StripePy is quick and easy using pip:

bash pip install 'stripepy-hic[all]'

For other installation options (conda, source, and Docker or Singularity/Apptainer), and details on ensuring StripePy is in your PATH, please refer to the official documentation.

Why Choose StripePy?

StripePy stands out with several key features that make it a fast and robust stripe caller:

Broad Format Support: Compatible with major formats: .hic, .cool and .mcool; outputs to .hdf5 and BEDPE.
User-Friendly: Designed with an intuitive command-line interface, making stripe analysis accessible even to less experienced users.
Stripe descriptors: Computes stripe width, height, and generates various statistics for post-processing, e.g., ranking and filtering.
Optimized performance: Outperforms other tools over diverse datasets and a simulated benchmark, StripeBench.
Exceptional speed & Low Memory: Significantly faster than existing tools (2x Chromosight, 66x Stripenn), with much lower memory usage.

Key Features

StripePy is organized into a few subcommands:

stripepy download: download a minified sample dataset suitable to quickly test StripePy - link.
stripepy call: run the stripe detection algorithm and store the identified stripes in a .hdf5 file - link.
stripepy view: take the result.hdf5 file generated by stripepy call and extract stripes in BEDPE format - link.
stripepy plot: generate various kinds of plots to inspect the stripes identified by stripepy call- link.

For a quick introduction to the tool, refer to the Quickstart section in the documentation.

Graphical Abstract

For more information on the subcommands, please run stripepy --help and refer to the documentation and the paper.

Getting help

For any issues regarding StripePy installation, walkthrough, and output interpretation please open a discussion on GitHub.

If you've found a bug or would like to suggest a new feature, please open a new issue instead.

Citing

If you use StripePy in your research, please cite the following publication:

Andrea Raffo, Roberto Rossini, Jonas Paulsen\ StripePy: fast and robust characterization of architectural stripes\ Bioinformatics, Volume 41, Issue 6, June 2025, btaf351\ https://doi.org/10.1093/bioinformatics/btaf351

BibTex

```bibtex @article{stripepy, author = {Raffo, Andrea and Rossini, Roberto and Paulsen, Jonas}, title = {{StripePy: fast and robust characterization of architectural stripes}}, journal = {Bioinformatics}, volume = {41}, number = {6}, pages = {btaf351}, year = {2025}, month = {06}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btaf351}, url = {https://doi.org/10.1093/bioinformatics/btaf351}, eprint = {https://academic.oup.com/bioinformatics/article-pdf/41/6/btaf351/63484367/btaf351.pdf}, } ```

Owner

Name: paulsengroup
Login: paulsengroup
Kind: organization

Repositories: 3
Profile: https://github.com/paulsengroup

Citation (CITATION.cff)

# Copyright (C) 2024 Roberto Rossini <roberros@uio.no>
#
# SPDX-License-Identifier: MIT

cff-version: 1.2.0
message: 'If you use this software, please cite it using the metadata from this file.'
authors:
  - given-names: Andrea
    family-names: Raffo
    orcid: 'https://orcid.org/0000-0003-3559-0533'
    email: andrea.raffo@ibv.uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
  - given-names: Roberto
    family-names: Rossini
    orcid: 'https://orcid.org/0000-0003-3096-1470'
    email: roberros@uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
title: StripePy
abstract: 'StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning'
doi: '10.5281/zenodo.14394041'
url: 'https://github.com/paulsengroup/StripePy'
repository-code: 'https://github.com/paulsengroup/StripePy'
repository-artifact: 'https://github.com/paulsengroup/StripePy/pkgs/container/stripepy'
type: software
license: MIT
keywords:
  - architectural-stripes
  - bioinformatics
  - cli-application
  - hi-c
  - loop-extrusion
  - python

preferred-citation:
  type: article
  authors:
  - given-names: Andrea
    family-names: Raffo
    orcid: 'https://orcid.org/0000-0003-3559-0533'
    email: andrea.raffo@ibv.uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
  - given-names: Roberto
    family-names: Rossini
    orcid: 'https://orcid.org/0000-0003-3096-1470'
    email: roberros@uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
  - given-names: Jonas
    family-names: Paulsen
    orcid: 'https://orcid.org/0000-0002-7918-5495'
    email: jonas.paulsen@ibv.uio.no
    affiliation: 'Department of Biosciences, University of Oslo'
  doi: '10.1093/bioinformatics/btaf351'
  url: 'https://doi.org/10.1093/bioinformatics/btaf351'
  journal: 'Bioinformatics'
  issn: '1367-4811'
  year: 2025
  month: 06
  title: 'StripePy: fast and robust characterization of architectural stripes'
  abstract: >
    Architectural stripes in Hi-C and related data are crucial for gene regulation, development, and DNA repair.
    Despite their importance, few tools exist for automatic stripe detection.
    We introduce StripePy, which leverages computational geometry methods to identify and analyze architectural stripes in contact maps from Chromosome Conformation Capture experiments like Hi-C and Micro-C.
    StripePy outperforms existing tools, as shown through tests on various datasets and a newly developed simulated benchmark, StripeBench, providing a valuable resource for the community.

references:
  - authors:
    - given-names: Andrea
      family-names: Raffo
      orcid: 'https://orcid.org/0000-0003-3559-0533'
      email: andrea.raffo@ibv.uio.no
      affiliation: 'Department of Biosciences, University of Oslo'
    - given-names: Roberto
      family-names: Rossini
      orcid: 'https://orcid.org/0000-0003-3096-1470'
      email: roberros@uio.no
      affiliation: 'Department of Biosciences, University of Oslo'
    - given-names: Jonas
      family-names: Paulsen
      orcid: 'https://orcid.org/0000-0002-7918-5495'
      email: jonas.paulsen@ibv.uio.no
      affiliation: 'Department of Biosciences, University of Oslo'
    type: article
    doi: '10.1101/2024.12.20.629789'
    url: 'https://www.biorxiv.org/content/early/2024/12/22/2024.12.20.629789'
    journal: 'Cold Spring Harbor Laboratory'
    year: 2024
    month: 12
    title: 'StripePy: fast and robust characterization of architectural stripes'
    abstract: >
      Architectural stripes in Hi-C and related data are crucial for gene regulation, development, and DNA repair.
      Despite their importance, few tools exist for automatic stripe detection.
      We introduce StripePy, which leverages computational geometry methods to identify and analyze architectural stripes in contact maps from Chromosome Conformation Capture experiments like Hi-C and Micro-C.
      StripePy outperforms existing tools, as shown through tests on various datasets and a newly developed simulated benchmark, StripeBench, providing a valuable resource for the community.

GitHub Events

Total

Create event: 38
Release event: 5
Issues event: 29
Watch event: 7
Delete event: 27
Issue comment event: 96
Push event: 145
Public event: 1
Pull request review comment event: 5
Pull request review event: 96
Pull request event: 260
Fork event: 2

Last Year

Create event: 38
Release event: 5
Issues event: 29
Watch event: 7
Delete event: 27
Issue comment event: 96
Push event: 145
Public event: 1
Pull request review comment event: 5
Pull request review event: 96
Pull request event: 260
Fork event: 2

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 6
Total pull requests: 92
Average time to close issues: 2 months
Average time to close pull requests: 7 days
Total issue authors: 1
Total pull request authors: 5
Average comments per issue: 0.0
Average comments per pull request: 0.79
Merged pull requests: 51
Bot issues: 0
Bot pull requests: 30

Past Year

Issues: 6
Pull requests: 92
Average time to close issues: 2 months
Average time to close pull requests: 7 days
Issue authors: 1
Pull request authors: 5
Average comments per issue: 0.0
Average comments per pull request: 0.79
Merged pull requests: 51
Bot issues: 0
Bot pull requests: 30

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Top Authors

Issue Authors

robomics (17)

Pull Request Authors

robomics (71)
dependabot[bot] (29)
rea1991 (28)
obikenobi23 (7)
pre-commit-ci[bot] (2)

Top Labels

Issue Labels

enhancement (8) testing (5) documentation (3) dependencies (2) bug (1) refactor (1)

Pull Request Labels

enhancement (43) dependencies (37) bug (20) documentation (17) refactor (17) testing (14) github_actions (7) parameters (4) python (2)

Packages

Total packages: 1
Total downloads:
- pypi 13 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 5
Total maintainers: 2

pypi.org: stripepy-hic

StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning

Homepage: https://github.com/paulsengroup/StripePy
Documentation: https://stripepy-hic.readthedocs.io/
License: mit
Latest release: 1.1.1
published 6 months ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 13 Last month

Rankings

Dependent packages count: 10.3%

Average: 34.1%

Dependent repos count: 57.9%

Maintainers (2)

robomics rea191

Last synced: 5 months ago

Dependencies

.github/workflows/ci.yml actions

actions/checkout v4 composite
actions/github-script v7 composite
actions/setup-python v5 composite

pyproject.toml pypi

bioframe >0.7, <1
h5py >3, <4
hictkpy [scipy] >=1, <2
matplotlib >=3.8, <4
numpy >=1.26, <2
pandas >=2.0, <3
scikit-learn >=1.5, <2
scipy >=1.10, <2
seaborn >=0.13, <1

src/stripepy/cli/setup.py pypi

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Open Source Science

stripepy-hic

Science Score: 67.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

StripePy

Why Choose StripePy?

Key Features

Getting help

Citing

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Issues and Pull Requests

All Time

Past Year

Top Authors

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pypi.org: stripepy-hic

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Maintainers (2)

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