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pyteomics

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.

https://github.com/levitsky/pyteomics

Science Score: 36.0%

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
  • ✓
    Committers with academic emails
    2 of 23 committers (8.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary

Keywords from Contributors

bioinformatics genomics ngs proteomics
Last synced: 10 months ago · JSON representation

Repository

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.

Basic Info
Statistics
  • Stars: 138
  • Watchers: 7
  • Forks: 38
  • Open Issues: 7
  • Releases: 25
Created over 6 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License Authors

README.rst 

.. image:: https://github.com/levitsky/pyteomics/workflows/tests/badge.svg
   :target: https://github.com/levitsky/pyteomics/actions?query=workflow%3Atests
   :alt: Test status

.. image:: https://img.shields.io/pypi/v/pyteomics.svg
    :target: https://pypi.org/project/pyteomics/
    :alt: PyPI

.. image:: https://img.shields.io/conda/vn/bioconda/pyteomics
    :target: http://bioconda.github.io/recipes/pyteomics/README.html
    :alt: conda

.. image:: https://img.shields.io/readthedocs/pyteomics.svg
    :target: https://pyteomics.readthedocs.io/
    :alt: Read the Docs (latest)

.. image:: https://img.shields.io/github/license/levitsky/pyteomics
    :target: https://www.apache.org/licenses/LICENSE-2.0
    :alt: Apache License

.. image:: https://img.shields.io/aur/version/python-pyteomics.svg
    :target: https://aur.archlinux.org/packages/python-pyteomics/
    :alt: python-pyteomics on AUR

.. image:: https://img.shields.io/badge/pyteomics-awesome-orange.svg
    :alt: Pyteomics is awesome


What is Pyteomics?
------------------

Pyteomics is a collection of lightweight and handy tools for Python that help
to handle various sorts of proteomics data. Pyteomics provides a growing set of
modules to facilitate the most common tasks in proteomics data analysis, such as:

* calculation of basic physico-chemical properties of polypeptides:

  * mass and isotopic distribution
  * charge and pI
  * chromatographic retention time

* access to common proteomics data:

  * MS or LC-MS data
  * FASTA databases
  * search engines output

* easy manipulation of sequences of modified peptides and proteins

The goal of the Pyteomics project is to provide a versatile, reliable and
well-documented set of open tools for the wide proteomics community.
One of the project's key features is Python itself, an open source language
increasingly popular in scientific programming. The main
applications of the library are reproducible statistical data analysis and rapid
software prototyping.

Owner

  • Name: Lev Levitsky
  • Login: levitsky
  • Kind: user
  • Location: Moscow, Russia

GitHub Events

Total
  • Issues event: 16
  • Watch event: 20
  • Delete event: 6
  • Issue comment event: 43
  • Push event: 46
  • Pull request review event: 15
  • Pull request review comment event: 15
  • Pull request event: 14
  • Fork event: 4
  • Create event: 4
Last Year
  • Issues event: 16
  • Watch event: 20
  • Delete event: 6
  • Issue comment event: 43
  • Push event: 46
  • Pull request review event: 15
  • Pull request review comment event: 15
  • Pull request event: 14
  • Fork event: 4
  • Create event: 4

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 1,708
  • Total Committers: 23
  • Avg Commits per committer: 74.261
  • Development Distribution Score (DDS): 0.197
Past Year
  • Commits: 79
  • Committers: 4
  • Avg Commits per committer: 19.75
  • Development Distribution Score (DDS): 0.101
Top Committers
Name Email Commits
Lev Levitsky 3****y 1,371
Joshua Klein m****n@g****m 213
Anton Goloborodko g****n@g****m 70
Anna Lefarova a****a@g****m 8
Mark Ivanov m****t 6
Julian Mueller j****r@i****m 5
Fabian Egli f****i 5
Julia Bubis 3****r 4
caetera h****k@g****m 4
Lev Levitsky l****y@p****u 3
Michael Porter 4****t 3
Dikshant jha 1****4 2
Donavan See d****n@s****m 2
Sean Peters 3****i 2
saulius s****s@c****n 2
Andrey Rozenberg a****h@g****m 1
Jim Johnson jj@u****u 1
John Chilton j****n@g****m 1
Manor Askenazi 5****r 1
Micha Birklbauer m****r@g****m 1
Ralf Gabriels r****g@h****e 1
Seth Just 9****o 1
superrino130 6****0 1
Committer Domains (Top 20 + Academic)
hotmail.be: 1 umn.edu: 1 ce-pdimaggi-04.ce.ic.ac.uk.localdomain: 1 see-empire.com: 1 phystech.su: 1 immatics.com: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 89
  • Total pull requests: 73
  • Average time to close issues: 28 days
  • Average time to close pull requests: 11 days
  • Total issue authors: 50
  • Total pull request authors: 15
  • Average comments per issue: 3.19
  • Average comments per pull request: 2.53
  • Merged pull requests: 71
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 14
  • Pull requests: 11
  • Average time to close issues: 10 days
  • Average time to close pull requests: 8 days
  • Issue authors: 10
  • Pull request authors: 3
  • Average comments per issue: 2.21
  • Average comments per pull request: 3.0
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • levitsky (9)
  • RalfG (6)
  • sorenwacker (5)
  • mobiusklein (4)
  • colin-combe (4)
  • caetera (4)
  • alessandro-vai (3)
  • jspaezp (3)
  • CCranney (3)
  • hguturu (3)
  • fabianegli (2)
  • morestart (2)
  • sjust-seerbio (2)
  • lutzfischer (2)
  • ypriverol (2)
Pull Request Authors
  • mobiusklein (43)
  • levitsky (27)
  • RalfG (4)
  • caetera (3)
  • fabianegli (2)
  • dikshant182004 (2)
  • alephreish (1)
  • superrino130 (1)
  • annalefarova (1)
  • donnyyy777 (1)
  • sjust-seerbio (1)
  • michabirklbauer (1)
  • paretje (1)
  • jmueller95 (1)
Top Labels
Issue Labels
documentation (1) enhancement (1) good first issue (1) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 87,085 last-month
  • Total docker downloads: 250,362
  • Total dependent packages: 52
  • Total dependent repositories: 110
  • Total versions: 77
  • Total maintainers: 2
pypi.org: pyteomics

A framework for proteomics data analysis.

  • Versions: 77
  • Dependent Packages: 52
  • Dependent Repositories: 110
  • Downloads: 87,085 Last month
  • Docker Downloads: 250,362
Rankings
Dependent packages count: 0.3%
Docker downloads count: 1.0%
Dependent repos count: 1.4%
Downloads: 2.4%
Average: 3.2%
Forks count: 7.1%
Stargazers count: 7.3%
Maintainers (2)
levitsky goloborodko.anton
Last synced: 10 months ago

Dependencies

doc/build-requirements.txt pypi
  • h5py *
  • lxml *
  • matplotlib *
  • sphinx-sitemap *
  • sqlalchemy *
requirements.txt pypi
  • lxml *
  • matplotlib *
  • numpy *
  • pandas *
  • pynumpress *
  • sqlalchemy *
test-requirements.txt pypi
  • cython * test
  • h5py * test
  • hdf5plugin <3.0.0 test
  • hdf5plugin * test
  • lxml * test
  • matplotlib * test
  • numpy * test
  • pandas * test
  • psims >0.1.42 test
  • pynumpress * test
  • sqlalchemy * test
.github/workflows/pythonpackage.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/pythonpublish.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
setup.py pypi