isocor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

Science Score: 39.0%

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Scientific vocabulary similarity
Low similarity (15.3%) to scientific vocabulary

Keywords

13c-mfa correction-natural-abundance fluxomics isotope isotope-correction isotope-labeling-experiments isotopic-inchi isotopologue-distribution mass-spectrometry metabolic-flux-analysis metabolomics ms-data

Last synced: 6 months ago · JSON representation

Repository

IsoCor: Isotope Correction for mass spectrometry labeling experiments

Basic Info

Host: GitHub
Owner: MetaSys-LISBP
License: gpl-3.0
Language: Python
Default Branch: master
Homepage: https://isocor.readthedocs.io
Size: 2.4 MB

Statistics

Stars: 24
Watchers: 3
Forks: 9
Open Issues: 6
Releases: 15

Topics

Created almost 8 years ago · Last pushed 10 months ago

Metadata Files

Readme License

README.md

IsoCor - Isotope Correction for mass spectrometry labeling experiments

What is IsoCor?

IsoCor is a scientific software dedicated to the correction of mass spectrometry (MS) data for naturally occuring isotopes. IsoCor corrects raw MS data (mass fractions) for naturally-occurring isotopes of all elements and purity of the isotopic tracer. The output of IsoCor is the isotopologue distribution of the molecule (i.e. the relative fractions of molecular entities differing only in the number of isotopic substitutions of the tracer). IsoCor also calculates the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites.

It is one of the routine tools that we use at the MetaSys team and MetaToul platform in isotopic studies of metabolic systems.

The code is open-source, and available under a GPLv3 license. Additional information can be found in IsoCor publication.

Detailed documentation can be found online at Read the Docs (https://isocor.readthedocs.io/). Check out the Tutorials to use the best correction option!

Key features

correction of naturally occuring isotopes, both for non-tracer and tracer elements,
correction of tracer purity,
shipped as a library with both a graphical and command line interface,
mass-spectrometer and resolution agnostic,
can be applied to singly- and multiply-charged ions
can be used with any tracer element (having two or more isotopes)
account for the contribution of derivatization steps (if any),
generate isotopic InChIs of tracer isotopologues,
open-source, free and easy to install everywhere where Python 3 and pip run,
biologist-friendly.

Quick-start

IsoCor requires Python 3.7 or higher and run on all platforms. Please check the documentation for complete installation and usage instructions.

Use pip to install IsoCor from PyPi:

bash $ pip install isocor

Then, start the graphical interface with:

bash $ isocor

IsoCor is also available directly from command-line and as a Python library.

Bug and feature requests

If you have an idea on how we could improve IsoCor please submit a new issue to our GitHub issue tracker.

Developers guide

Contributions

Contributions are very welcome! :heart:

Please work on your own fork, follow PEP8 style guide, and make sure you pass all the tests before a pull request.

Local install with pip

In development mode, do a pip install -e /path/to/IsoCor to install locally the development version.

Unit tests

Isotope correction is a complex task and we use unit tests to make sure that critical features are not compromised during development.

You can run all tests by calling pytest in the shell at project's root directory.

Build the documentation locally

Build the HTML documentation with:

bash $ cd doc $ make html

The PDF documentation can be built locally by replacing html by latexpdf in the command above. You will need a recent latex installation.

How to cite

Millard P., Delépine B., Guionnet M., Heuillet M., Bellvert F. and Letisse F. IsoCor: isotope correction for high-resolution MS labeling experiments. Bioinformatics, 2019, doi: 10.1093/bioinformatics/btz209

Authors

Baudoin Delépine, Matthieu Guionnet, Pierre Millard

Contact

:email: Pierre Millard, millard@insa-toulouse.fr

Owner

Name: MetaSys team (Toulouse Biotechnology Institute)
Login: MetaSys-LISBP
Kind: organization
Email: pierre.millard@insa-toulouse.fr
Location: Toulouse | France

Website: https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-metasys/
Twitter: PierreMillard
Repositories: 18
Profile: https://github.com/MetaSys-LISBP

Integrated METAbolism and dynamics of metabolic SYStems

GitHub Events

Total

Create event: 1
Issues event: 1
Release event: 1
Push event: 12
Pull request event: 6

Last Year

Create event: 1
Issues event: 1
Release event: 1
Push event: 12
Pull request event: 6

Committers

Last synced: over 2 years ago

All Time

Total Commits: 198
Total Committers: 8
Avg Commits per committer: 24.75
Development Distribution Score (DDS): 0.429

Past Year

Commits: 15
Committers: 2
Avg Commits per committer: 7.5
Development Distribution Score (DDS): 0.067

Top Committers

Name	Email	Commits
millard	m**d@i**r	113
Baudoin Delépine	b**e@g**m	27
pierremillard	m**d@i**r	22
llegregam	l**m@i**r	14
Matthieu Guionnet	g**t@i**r	12
Baudoin Delépine	d**e@i**r	7
gmat	g**k@y**r	2
Matthieu Guionnet	g**t@i**r	1

Committer Domains (Top 20 + Academic)

insa-toulouse.fr: 4 insat.insa-toulouse.fr: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 21
Total pull requests: 28
Average time to close issues: 3 months
Average time to close pull requests: about 19 hours
Total issue authors: 16
Total pull request authors: 4
Average comments per issue: 3.57
Average comments per pull request: 0.29
Merged pull requests: 25
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 6
Average time to close issues: 16 days
Average time to close pull requests: less than a minute
Issue authors: 1
Pull request authors: 2
Average comments per issue: 1.0
Average comments per pull request: 0.0
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

gmat (3)
XiaoyangSu (2)
pierremillard (2)
jmmitc06 (2)
jabnremtp (1)
litali (1)
liaochen1988 (1)
chuyaowang (1)
sebschmpi (1)
CIRCLE123567 (1)
hechth (1)
vcharlestin (1)
bowenli37 (1)
AndrewRosko (1)
ondrej-kuda (1)

Pull Request Authors

llegregam (10)
pierremillard (7)
gmat (5)
bdelepine (4)

Top Labels

Issue Labels

solved (5) bug (5) question (4) enhancement (4) help wanted (1) duplicate (1)

Pull Request Labels

bug (1) enhancement (1)

Packages

Total packages: 1
Total downloads:
- pypi 359 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 15
Total maintainers: 4

pypi.org: isocor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

Homepage: https://github.com/MetaSys-LISBP/IsoCor/
Documentation: https://isocor.readthedocs.io/
License: GNU General Public License v3 or later (GPLv3+)
Latest release: 2.2.3
published 10 months ago

Versions: 15
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 359 Last month

Rankings

Dependent packages count: 9.6%

Forks count: 12.0%

Stargazers count: 13.1%

Average: 14.6%

Downloads: 16.3%

Dependent repos count: 21.9%

Maintainers (4)

Lolopopo bdelepine gmat millard

Last synced: 6 months ago

Dependencies

requirements.txt pypi

autodoc *
ipykernel *
jupyter_client *
nbsphinx *
pandas >=0.17.1
pytest *
scipy >=0.12.1
sphinx >=1.4
sphinx-argparse *
sphinx-rtd-theme *
sphinxcontrib-napoleon *

.github/workflows/pypi_deployment.yml actions

actions/checkout master composite
actions/setup-python v1 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/test_suite.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

pyproject.toml pypi