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https://github.com/bigbio/quantms.io

The proteomics quantification format, extending mzTab for large scale datasets.

https://github.com/bigbio/quantms.io

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.3%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

The proteomics quantification format, extending mzTab for large scale datasets.

Basic Info
  • Host: GitHub
  • Owner: bigbio
  • License: other
  • Language: Python
  • Default Branch: main
  • Size: 370 MB
Statistics
  • Stars: 12
  • Watchers: 8
  • Forks: 6
  • Open Issues: 27
  • Releases: 2
Created about 3 years ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

quantms.io

Python application Upload Python Package Codacy Badge Codacy Badge PyPI version

The specification of quantms.io is a community-driven effort to create a standard for the representation of quantitative proteomics data. The specification is designed to be simple to implement and to be able to represent the most common types of quantitative proteomics data. The specification is designed to be extensible, and the full specification can be found in the specification document.

Core contributors and collaborators

The project is run by different groups:

  • Yasset Perez-Riverol (PRIDE Team, European Bioinformatics Institute - EMBL-EBI, U.K.)
  • Ping Zheng (Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China)

IMPORTANT: If you contribute with the following specification, please make sure to add your name to the list of contributors.

Code of Conduct

As part of our efforts toward delivering open and inclusive science, we follow the Contributor Covenant Code of Conduct for Open Source Projects.

How to cite

Copyright notice

This information is free; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This information is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this work; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

Owner

  • Name: BigBio Stack
  • Login: bigbio
  • Kind: organization
  • Email: proteomicsstack@gmail.com
  • Location: Cambridge, UK

Provide big data solutions Bioinformatics

GitHub Events

Total
  • Issues event: 18
  • Watch event: 4
  • Delete event: 3
  • Issue comment event: 105
  • Push event: 182
  • Pull request review comment event: 250
  • Pull request review event: 120
  • Pull request event: 24
  • Fork event: 3
Last Year
  • Issues event: 18
  • Watch event: 4
  • Delete event: 3
  • Issue comment event: 105
  • Push event: 182
  • Pull request review comment event: 250
  • Pull request review event: 120
  • Pull request event: 24
  • Fork event: 3

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 31
  • Total pull requests: 43
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 4 days
  • Total issue authors: 9
  • Total pull request authors: 8
  • Average comments per issue: 2.58
  • Average comments per pull request: 1.28
  • Merged pull requests: 28
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 18
  • Pull requests: 33
  • Average time to close issues: 18 days
  • Average time to close pull requests: 4 days
  • Issue authors: 7
  • Pull request authors: 7
  • Average comments per issue: 2.44
  • Average comments per pull request: 1.64
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ypriverol (18)
  • enryH (4)
  • timosachsenberg (2)
  • mobiusklein (2)
  • jgriss (1)
  • jpfeuffer (1)
  • h836472 (1)
  • WangHong007 (1)
  • jspaezp (1)
Pull Request Authors
  • ypriverol (16)
  • zprobot (10)
  • mobiusklein (6)
  • yueqixuan (5)
  • timosachsenberg (2)
  • Shen-YuFei (2)
  • enryH (1)
  • hjn0415a (1)
Top Labels
Issue Labels
enhancement (5) documentation (4) bug (2) no-priority (1)
Pull Request Labels
Review effort 3/5 (5) enhancement (5) documentation (4) Review effort 2/5 (3) tests (3) Review effort [1-5]: 4 (2) Review effort [1-5]: 2 (2) bug (1) good first issue (1) formatting (1) Bug fix (1) Review effort [1-5]: 5 (1) Review effort 4/5 (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 14 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
pypi.org: quantmsio

Convert multiple files into quantms.io format

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 14 Last month
Rankings
Dependent packages count: 9.6%
Average: 36.3%
Dependent repos count: 63.0%
Maintainers (1)
ypriverol
Last synced: 10 months ago

Dependencies

.github/workflows/python-app.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
docs/requirements.txt pypi
  • furo *
  • sphinx *
python/quantmsio/pyproject.toml pypi
python/quantmsio/requirements.txt pypi
  • biopython *
  • click *
  • datacompy *
  • diskcache *
  • numpy *
  • pandas *
  • pyarrow *
  • pyopenms *
  • requests *
  • scipy *
  • setuptools *
  • venn *
python/quantmsio/setup.py pypi
  • click *
  • diskcache *