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matchmsextras

additional network analysis functions for matchms

https://github.com/matchms/matchmsextras

Science Score: 57.0%

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 6 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

additional network analysis functions for matchms

Basic Info
  • Host: GitHub
  • Owner: matchms
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Size: 432 KB
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 2
  • Open Issues: 8
  • Releases: 9
Created over 5 years ago · Last pushed almost 3 years ago
Metadata Files
Readme Changelog License Citation

README.md

GitHub Workflow Status GitHub PyPI

matchmsextras

Additional functionalities to be used with matchms.

Usually this is stuff which either in scope and/or in code quality and/or in degree of unit testing does not match the criteria we have for matchms. For producing the results shown in our Spec2Vec article, PLoS Computational Biology, 2021 we used code from matchmsextras 0.1.0. To fully reproduce those results you can install this via pip install matchmsextras==0.1.0. For all other purposes we recommend using the latest release.

Installation

pip install matchmsextras

Citing us

If you use matchmsextras for your research, please cite the following references:

Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJJ, (2021) "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLoS Comput Biol 17(2): e1008724. https://doi.org/10.1371/journal.pcbi.1008724

F. Huber, S. Verhoeven, C. Meijer, H. Spreeuw, E. M. Villanueva Castilla, C. Geng, J.J.J. van der Hooft, S. Rogers, A. Belloum, F. Diblen, J.H. Spaaks, (2020). "matchms - processing and similarity evaluation of mass spectrometry data". Journal of Open Source Software, 5(52), 2411, https://doi.org/10.21105/joss.02411

Many extra thanks!

Tutorial on matchms and Spec2Vec

Possibly the easiest way to learn how to run matchmsextras is to follow our tutorial on matchms.

Owner

  • Name: matchms
  • Login: matchms
  • Kind: organization

Citation (CITATION.cff) 

# YAML 1.2
---
abstract: "Additional functions to be used with matchms."
authors:
  -
    affiliation: "Netherlands eScience Center"
    family-names: Huber
    given-names: Florian
    orcid: "https://orcid.org/0000-0002-3535-9406"

cff-version: "1.1.0"
license: "Apache-2.0"
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/matchms/matchmsextras"
title: matchmsextras

GitHub Events

Total
  • Issues event: 1
  • Fork event: 1
Last Year
  • Issues event: 1
  • Fork event: 1

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 87
  • Total Committers: 3
  • Avg Commits per committer: 29.0
  • Development Distribution Score (DDS): 0.149
Top Committers
Name Email Commits
florian-huber 3****r@u****m 74
florian-huber f****r@h****e 12
dianacarvalho1 d****a@d****m 1
Committer Domains (Top 20 + Academic)
datarevenue.com: 1 hs-duesseldorf.de: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 12
  • Total pull requests: 12
  • Average time to close issues: about 10 hours
  • Average time to close pull requests: 1 day
  • Total issue authors: 4
  • Total pull request authors: 3
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.17
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • florian-huber (5)
  • niekdejonge (2)
  • yoglo (1)
  • hechth (1)
Pull Request Authors
  • florian-huber (8)
  • niekdejonge (1)
  • dianacarvalho1 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 208 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
pypi.org: matchmsextras

Additional functionalities to be used with matchms

  • Versions: 7
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 208 Last month
Rankings
Dependent packages count: 4.8%
Downloads: 10.8%
Average: 15.9%
Forks count: 19.1%
Dependent repos count: 21.6%
Stargazers count: 23.1%
Maintainers (1)
florian-huber
Last synced: 10 months ago

Dependencies

setup.py pypi
  • matchms >=0.11.0
  • networkx *
  • pandas *
  • python-louvain *
  • spec2vec *
.github/workflows/CI_build.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
.github/workflows/CI_publish_pypi.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • pypa/gh-action-pypi-publish master composite