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iced

iced: fast and memory efficient normalization of contact maps - Published in JOSS (2019)

https://github.com/hiclib/iced

Science Score: 98.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

i

Scientific Fields

Mathematics Computer Science - 84% confidence
Artificial Intelligence and Machine Learning Computer Science - 83% confidence
Last synced: 4 months ago · JSON representation ·

Repository

Normalizing Hi-C contact counts efficiently

Basic Info
Statistics
  • Stars: 35
  • Watchers: 1
  • Forks: 21
  • Open Issues: 18
  • Releases: 0
Topics
i
Created almost 11 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.rst 

.. -*- mode: rst -*-

|Travis|_ |Coveralls|_

.. |Travis| image:: https://api.travis-ci.org/hiclib/iced.png?branch=master
.. _Travis: https://travis-ci.org/hiclib/iced

.. |Coveralls| image::
   https://coveralls.io/repos/github/hiclib/iced/badge.svg?branch=master
.. _Coveralls: https://coveralls.io/r/hiclib/iced?branch=master


iced
====

The python module iced implements the ICE normalization of hic data


Depends on

python >= 2.7
numpy >= 1.16
scipy >= 0.19
sklearn
pandas

Owner

  • Name: hiclib
  • Login: hiclib
  • Kind: organization

JOSS Publication

iced: fast and memory efficient normalization of contact maps
Published
April 03, 2019
DOI
Volume 4, Issue 36, Page 1286
Authors
Nelle Varoquaux ORCID
University of California, Berkeley
Nicolas Servant ORCID
Institut Curie, INSERM U900, Mines ParisTech
Editor
Pjotr Prins ORCID
Tags
Hi-C contact count Normalization
View PDF Review Thread Software Archive

Citation (CITATION) 

To reference iced in publication, please cite the following:

@Article{servant:hicpro,
   Author="Servant, N.  and Varoquaux, N.  and Lajoie, B. R.  and Viara, E.
   and Chen, C. J.  and Vert, J. P.  and Heard, E.  and Dekker, J.  and
   Barillot, E. ",
   Title="{{H}i{C}-{P}ro: an optimized and flexible pipeline for {H}i-{C} data processing}",
   Journal="Genome Biol.",
   Year="2015",
   Volume="16",
   Pages="259"
  }

GitHub Events

Total
  • Issues event: 3
  • Watch event: 8
  • Delete event: 1
  • Issue comment event: 4
  • Push event: 2
  • Pull request event: 6
  • Fork event: 1
  • Create event: 4
Last Year
  • Issues event: 3
  • Watch event: 8
  • Delete event: 1
  • Issue comment event: 4
  • Push event: 2
  • Pull request event: 6
  • Fork event: 1
  • Create event: 4

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 239
  • Total Committers: 6
  • Avg Commits per committer: 39.833
  • Development Distribution Score (DDS): 0.105
Past Year
  • Commits: 7
  • Committers: 2
  • Avg Commits per committer: 3.5
  • Development Distribution Score (DDS): 0.286
Top Committers
Name Email Commits
Nelle Varoquaux n****x@g****m 214
nservant n****t@c****r 11
Roberto Rossini 7****s 6
Gesine g****r 5
Thomas Gilgenast t****t@g****m 2
Matthias Blum m****m 1
Committer Domains (Top 20 + Academic)
curie.fr: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 27
  • Total pull requests: 76
  • Average time to close issues: 16 days
  • Average time to close pull requests: about 1 month
  • Total issue authors: 17
  • Total pull request authors: 5
  • Average comments per issue: 1.63
  • Average comments per pull request: 0.66
  • Merged pull requests: 67
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 months
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • NelleV (9)
  • robinweide (2)
  • biozzq (2)
  • lhanappa (1)
  • thomasgilgenast (1)
  • Balthasar-eu (1)
  • hanbinlu (1)
  • concatenize (1)
  • BioinformaticsXin (1)
  • werhoog (1)
  • QianzhaoJ (1)
  • diamondzabala1903-gif (1)
  • sshen82 (1)
  • esebesty (1)
  • beeber52 (1)
Pull Request Authors
  • NelleV (72)
  • nservant (3)
  • robomics (3)
  • gesinecauer (2)
  • thomasgilgenast (2)
Top Labels
Issue Labels
CRITICAL (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 281 last-month
  • Total docker downloads: 43
  • Total dependent packages: 2
  • Total dependent repositories: 9
  • Total versions: 25
  • Total maintainers: 1
pypi.org: iced

ICE normalization

  • Versions: 25
  • Dependent Packages: 2
  • Dependent Repositories: 9
  • Downloads: 281 Last month
  • Docker Downloads: 43
Rankings
Docker downloads count: 1.3%
Dependent packages count: 4.8%
Dependent repos count: 4.8%
Average: 6.9%
Downloads: 16.7%
Maintainers (1)
NelleV
Last synced: 4 months ago

Dependencies

requirements/default.txt pypi
  • cython *
  • numpy >=1.16
  • pandas *
  • scipy >=0.19
  • sklearn *
requirements/docs.txt pypi
  • matplotlib >=3.3
  • numpydoc >=1.0
  • sphinx >=1.8
  • sphinx-gallery >=0.7.0,
requirements/tests.txt pypi
  • codecov *
  • flake8 *
  • pytest >=5.2.0
  • pytest-cov >=2.7.0
.github/workflows/build-doc.yml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v1 composite
.github/workflows/test.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
iced/datasets/setup.py pypi
iced/io/setup.py pypi
iced/setup.py pypi
pyproject.toml pypi
requirements.txt pypi
setup.py pypi
environment.yml conda
  • cython
  • numpy >1.16
  • pandas
  • python >3
  • scikit-learn
  • scipy >0.19