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mass-tools

Various projects dealing with molecular formula

https://github.com/cheminfo/mass-tools

Science Score: 67.0%

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 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.2%) to scientific vocabulary

Keywords

hacktoberfest
Last synced: 6 months ago · JSON representation ·

Repository

Various projects dealing with molecular formula

Basic Info
Statistics
  • Stars: 8
  • Watchers: 4
  • Forks: 0
  • Open Issues: 25
  • Releases: 275
Topics
hacktoberfest
Created over 8 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Citation

README.md

mass-tools

NPM version build status Test coverage DOI

Various tools allowing to manipulate molecular formula and analyse mass spectra.

The library is published as a full package on npm as mass-tools.

It is also published for the browser on the CDN https://www.lactame.com.

The library contains the following tools:

  • EMDB: database of molecular formula
  • Groups: List of groups understood by the package
  • Elements: Periodic table elements with associated mw and atomic mass
  • IsotopicDistribution: Package to create isotopic distribution
  • MF: Parse and format molecular formula
  • Peptide: Parse peptide sequences
  • Nucleotide: Parse nucleic sequences
  • Spectrum: Deal with mass spectrum
  • getPeaks: Filter array of peaks
  • getBestPeaks: Get the best peaks of an array of peaks
  • generateMFs: Generate all possible molecular formula
  • Report: Generate fragmentation reports
  • atomSorter: Sort symbol of atoms
  • mfFromEA: Determine molecular formula from elemental analysis

This package should not be installed as we provide many specific packages with the different tools.

  • EMDB: npm i emdb
  • Elements / Groups: npm i chemical-groups
  • IsotopicDistribution: npm i isotopic-distribution
  • MF: npm i mf-parser
  • Peptide: npm i peptide
  • Nucleotide: npm i nucleotide
  • Spectrum: npm i ms-spectrum
  • generateMFs: npm i mf-generator
  • Report: npm i ms-report
  • atomSorter: npm i atom-sorter

Monorepo

npm install <dependency> -w <package>

License

MIT

Owner

  • Name: Cheminfo
  • Login: cheminfo
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: 'If you use this software, please cite it as below.'
title: 'Javascript libraries dealing with mass spectra'
abstract: 'This lerna project contains various packages that allows to manipulate molecular formula, peptide and nucleotide sequences and assign high resolution mass spectra'
repository-artifact: http://cheminfo.github.io/mass-tools/
repository-code: https://github.com/cheminfo/mass-tools
authors:
  - family-names: 'Patiny'
    given-names: 'Luc'
    affiliation: 'Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland'
    orcid: 'https://orcid.org/0000-0002-4943-2643'
  - family-names: 'Zasso'
    given-names: 'Michaël'
    affiliation: 'Zakodium Sàrl, Switzerland'
    orcid: 'https://orcid.org/0000-0001-5295-2159'
  - family-names: 'Silvestre'
    given-names: 'Ricardo'
    affiliation: 'Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland'
    orcid: 'https://orcid.org/0000-0002-5372-6716'
license: MIT
keywords:
  - Mass spectra
  - Molecular formula
doi: 10.5281/zenodo.5091564

GitHub Events

Total
  • Create event: 66
  • Issues event: 30
  • Release event: 17
  • Delete event: 45
  • Member event: 1
  • Issue comment event: 111
  • Push event: 150
  • Pull request review event: 14
  • Pull request review comment event: 8
  • Pull request event: 93
Last Year
  • Create event: 66
  • Issues event: 30
  • Release event: 17
  • Delete event: 45
  • Member event: 1
  • Issue comment event: 111
  • Push event: 150
  • Pull request review event: 14
  • Pull request review comment event: 8
  • Pull request event: 93

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 1,612
  • Total Committers: 6
  • Avg Commits per committer: 268.667
  • Development Distribution Score (DDS): 0.331
Past Year
  • Commits: 134
  • Committers: 4
  • Avg Commits per committer: 33.5
  • Development Distribution Score (DDS): 0.575
Top Committers
Name Email Commits
Luc Patiny l****c@p****m 1,078
cheminfo-bot 1****t 392
RicardoSilvestr r****r@h****h 103
Michaël Zasso t****s@p****m 31
tpoisseau 2****u 5
Luc Patiny l****y@L****l 3
Committer Domains (Top 20 + Academic)
hes-so.ch: 1 patiny.com: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 48
  • Total pull requests: 226
  • Average time to close issues: 6 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 6
  • Total pull request authors: 5
  • Average comments per issue: 1.19
  • Average comments per pull request: 1.41
  • Merged pull requests: 211
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 19
  • Pull requests: 57
  • Average time to close issues: 3 days
  • Average time to close pull requests: 2 days
  • Issue authors: 4
  • Pull request authors: 4
  • Average comments per issue: 1.32
  • Average comments per pull request: 1.54
  • Merged pull requests: 50
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lpatiny (19)
  • targos (15)
  • tpoisseau (5)
  • stropitek (5)
  • RicardoSilvestr (3)
  • jdesport (2)
  • cheminfo-bot (1)
Pull Request Authors
  • cheminfo-bot (187)
  • lpatiny (61)
  • targos (25)
  • tpoisseau (11)
  • RicardoSilvestr (5)
Top Labels
Issue Labels
autorelease: pending (1)
Pull Request Labels
autorelease: tagged (142) autorelease: pending (45) hacktoberfest-accepted (1)

Packages

  • Total packages: 23
  • Total downloads:
    • npm 37,361 last-month
  • Total dependent packages: 146
    (may contain duplicates)
  • Total dependent repositories: 142
    (may contain duplicates)
  • Total versions: 1,764
  • Total maintainers: 4
npmjs.org: mf-parser

Parse a molecular formula

  • Versions: 79
  • Dependent Packages: 24
  • Dependent Repositories: 17
  • Downloads: 7,052 Last month
Rankings
Dependent packages count: 1.1%
Downloads: 2.0%
Dependent repos count: 3.0%
Average: 6.5%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: chemical-elements

JSON containing information about chemical elements and isotopes

  • Versions: 55
  • Dependent Packages: 11
  • Dependent Repositories: 14
  • Downloads: 6,419 Last month
Rankings
Dependent packages count: 1.9%
Downloads: 2.0%
Dependent repos count: 3.3%
Average: 6.8%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: atom-sorter

Callback allowing to sort chemical elements (atoms) in Hill order

  • Versions: 40
  • Dependent Packages: 10
  • Dependent Repositories: 20
  • Downloads: 7,182 Last month
Rankings
Downloads: 1.9%
Dependent repos count: 2.8%
Dependent packages count: 3.1%
Average: 6.9%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: chemical-groups

JSON containing information about chemical groups

  • Versions: 27
  • Dependent Packages: 8
  • Dependent Repositories: 13
  • Downloads: 6,168 Last month
Rankings
Downloads: 2.1%
Dependent packages count: 2.4%
Dependent repos count: 3.4%
Average: 6.9%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: ms-spectrum

A mass spectrum

  • Versions: 119
  • Dependent Packages: 9
  • Dependent Repositories: 8
  • Downloads: 962 Last month
Rankings
Dependent packages count: 2.3%
Downloads: 2.8%
Dependent repos count: 4.1%
Average: 7.0%
Stargazers count: 10.4%
Forks count: 15.4%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mf-utilities

Small utilities dealing with molecular formula

  • Versions: 75
  • Dependent Packages: 18
  • Dependent Repositories: 7
  • Downloads: 1,469 Last month
Rankings
Dependent packages count: 1.3%
Downloads: 2.9%
Dependent repos count: 4.5%
Average: 7.1%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: isotopic-distribution

Calculate the isotopic distribution of a molecular formula

  • Versions: 96
  • Dependent Packages: 8
  • Dependent Repositories: 10
  • Downloads: 900 Last month
Rankings
Dependent packages count: 2.7%
Downloads: 3.6%
Dependent repos count: 3.8%
Average: 7.3%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mf-generator

Generate molecular formula based on a range and filters

  • Versions: 100
  • Dependent Packages: 9
  • Dependent Repositories: 8
  • Downloads: 638 Last month
Rankings
Dependent packages count: 2.4%
Downloads: 3.5%
Dependent repos count: 4.2%
Average: 7.4%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: peptide

Peptide

  • Versions: 46
  • Dependent Packages: 7
  • Dependent Repositories: 8
  • Downloads: 552 Last month
Rankings
Dependent packages count: 2.7%
Downloads: 3.6%
Dependent repos count: 4.2%
Average: 7.4%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: emdb

Database manager for exact mass query

  • Versions: 143
  • Dependent Packages: 4
  • Dependent Repositories: 6
  • Downloads: 537 Last month
Rankings
Downloads: 2.7%
Dependent packages count: 4.5%
Dependent repos count: 4.6%
Average: 7.5%
Stargazers count: 10.4%
Forks count: 15.4%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mf-matcher

Returns true / false for an object using mw, em, msem, unsaturation and atoms

  • Versions: 85
  • Dependent Packages: 5
  • Dependent Repositories: 6
  • Downloads: 916 Last month
Rankings
Dependent packages count: 3.6%
Downloads: 3.6%
Dependent repos count: 4.8%
Average: 7.7%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: nucleotide

Deal with nucleotides and molecular formula

  • Versions: 72
  • Dependent Packages: 5
  • Dependent Repositories: 6
  • Downloads: 463 Last month
Rankings
Dependent packages count: 3.6%
Downloads: 3.7%
Dependent repos count: 4.8%
Average: 7.7%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mf-finder

Find a molecular formula from a monoisotopic mass

  • Versions: 90
  • Dependent Packages: 5
  • Dependent Repositories: 6
  • Downloads: 913 Last month
Rankings
Downloads: 3.5%
Dependent packages count: 4.4%
Dependent repos count: 4.8%
Average: 7.9%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mf-from-google-sheet

Retrieve and format molecular formula from google sheet

  • Versions: 100
  • Dependent Packages: 3
  • Dependent Repositories: 6
  • Downloads: 546 Last month
Rankings
Downloads: 3.6%
Dependent repos count: 4.8%
Dependent packages count: 5.8%
Average: 8.2%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mass-tools

Many tools allowing to analyze mass spectra

  • Versions: 129
  • Dependent Packages: 4
  • Dependent Repositories: 2
  • Downloads: 398 Last month
Rankings
Downloads: 4.1%
Dependent packages count: 4.5%
Dependent repos count: 7.6%
Average: 8.4%
Stargazers count: 10.4%
Forks count: 15.4%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mf-global

Various libraries to deal with molecular formula and mass spectra

  • Versions: 127
  • Dependent Packages: 3
  • Dependent Repositories: 1
  • Downloads: 322 Last month
Rankings
Downloads: 4.4%
Dependent packages count: 5.9%
Average: 9.3%
Dependent repos count: 10.3%
Stargazers count: 10.4%
Forks count: 15.4%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mass-fragmentation

Code to fragment molecules

  • Versions: 46
  • Dependent Packages: 4
  • Dependent Repositories: 1
  • Downloads: 459 Last month
Rankings
Downloads: 3.5%
Dependent packages count: 5.8%
Average: 9.3%
Dependent repos count: 10.7%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: ms-report

Generate report for mass analysis

  • Versions: 75
  • Dependent Packages: 3
  • Dependent Repositories: 1
  • Downloads: 411 Last month
Rankings
Dependent packages count: 5.8%
Downloads: 7.7%
Average: 10.1%
Dependent repos count: 10.7%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mf-from-ea

Find a molecular formula from elemental analysis results

  • Versions: 54
  • Dependent Packages: 3
  • Dependent Repositories: 1
  • Downloads: 221 Last month
Rankings
Dependent packages count: 5.8%
Downloads: 9.9%
Average: 10.6%
Dependent repos count: 10.7%
Stargazers count: 10.7%
Forks count: 15.9%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: number-treemap

Manage a sorted tree of numbers

  • Versions: 75
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 222 Last month
Rankings
Dependent repos count: 10.7%
Stargazers count: 10.7%
Downloads: 11.5%
Average: 14.0%
Forks count: 15.9%
Dependent packages count: 21.1%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: octochemdb

Helper that allows to query the OctoChemDB webservices

  • Versions: 58
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 201 Last month
Rankings
Downloads: 9.8%
Stargazers count: 10.8%
Forks count: 15.7%
Average: 21.4%
Dependent repos count: 21.8%
Dependent packages count: 49.1%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mf-from-atomic-ratio

Find a molecular formula from atomic ratio

  • Versions: 19
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 177 Last month
Rankings
Stargazers count: 9.0%
Forks count: 13.6%
Average: 23.0%
Dependent repos count: 28.3%
Dependent packages count: 41.2%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago
npmjs.org: mfs-deconvolution
  • Versions: 54
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 233 Last month
Rankings
Stargazers count: 10.8%
Forks count: 15.7%
Downloads: 18.8%
Dependent repos count: 21.8%
Average: 23.2%
Dependent packages count: 49.1%
Maintainers (4)
cheminfo-bot targos lpatiny stropitek
Last synced: 7 months ago

Dependencies

package.json npm
  • @types/jest ^27.4.1 development
  • benchmark ^2.1.4 development
  • chemcalc ^3.4.1 development
  • chemical-elements ^1.2.1 development
  • cheminfo-build ^1.1.11 development
  • documentation ^13.2.5 development
  • eslint ^8.11.0 development
  • eslint-config-cheminfo ^7.3.0 development
  • jest ^27.5.1 development
  • jest-matcher-deep-close-to ^3.0.2 development
  • lerna ^4.0.0 development
  • prettier ^2.6.1 development
packages/chemical-elements/package.json npm
  • cross-fetch ^3.1.5 development
  • wikidata-sdk ^7.14.4 development
  • papaparse ^5.3.2
packages/emdb/package.json npm
  • jest-matcher-deep-close-to ^3.0.2 development
  • xy-parser ^5.0.2 development
  • chemical-elements ^1.2.3
  • chemical-groups ^1.2.1
  • cross-fetch ^3.1.5
  • isotopic-distribution ^1.4.12
  • jszip ^3.7.1
  • mf-finder ^1.2.10
  • mf-from-google-sheet ^1.1.34
  • mf-generator ^1.3.22
  • mf-matcher ^1.2.5
  • mf-parser ^1.4.7
  • mf-utilities ^1.3.3
  • ml-array-max ^1.2.4
  • ml-array-min ^1.2.3
  • ml-regression-theil-sen ^2.0.0
  • ms-spectrum ^1.6.9
  • nucleotide ^1.2.21
  • peaks-similarity ^2.3.1
  • peptide ^1.11.4
packages/isotopic-distribution/package.json npm
  • jest-matcher-deep-close-to ^3.0.2 development
  • chemical-elements ^1.2.3
  • mf-parser ^1.4.7
  • mf-utilities ^1.3.3
  • spectrum-generator ^8.0.1
packages/mass-tools/package.json npm
  • atom-sorter ^1.1.10
  • chemical-elements ^1.2.3
  • chemical-groups ^1.2.1
  • emdb ^1.10.2
  • isotopic-distribution ^1.4.12
  • mf-from-ea ^0.0.22
  • mf-generator ^1.3.22
  • mf-parser ^1.4.7
  • ms-report ^1.4.3
  • ms-spectrum ^1.6.9
  • nucleotide ^1.2.21
  • peaks-similarity ^2.3.1
  • peptide ^1.11.4
  • sum-object-keys ^1.0.2
packages/mf-finder/package.json npm
  • atom-sorter ^1.1.10
  • chemical-elements ^1.2.3
  • mf-matcher ^1.2.5
  • mf-parser ^1.4.7
  • mf-utilities ^1.3.3
packages/mf-from-ea/package.json npm
  • jest-matcher-deep-close-to ^3.0.2 development
  • atom-sorter ^1.1.10
  • chemical-elements ^1.2.3
  • mf-parser ^1.4.7
  • mf-utilities ^1.3.3
packages/mf-from-google-sheet/package.json npm
  • mf-generator ^1.3.22
  • mf-parser ^1.4.7
  • mf-utilities ^1.3.3
  • papaparse ^5.3.2
  • request ^2.88.2
  • request-promise-native ^1.0.9
packages/mf-generator/package.json npm
  • jest-matcher-deep-close-to ^3.0.2 development
  • chemical-elements ^1.2.3
  • mf-finder ^1.2.10
  • mf-matcher ^1.2.5
  • mf-parser ^1.4.7
  • mf-utilities ^1.3.3
  • sum-object-keys ^1.0.2
packages/mf-global/package.json npm
  • chemical-elements ^1.2.3
  • chemical-groups ^1.2.1
  • emdb ^1.10.2
  • isotopic-distribution ^1.4.12
  • mf-generator ^1.3.22
  • mf-parser ^1.4.7
  • ms-report ^1.4.3
  • ms-spectrum ^1.6.9
  • nucleotide ^1.2.21
  • peptide ^1.11.4
packages/mf-matcher/package.json npm
  • jest-matcher-deep-close-to ^3.0.2 development
  • mf-utilities ^1.3.3
  • ml-spectra-processing ^11.1.0
packages/mf-parser/package.json npm
  • jest-matcher-deep-close-to ^3.0.2 development
  • atom-sorter ^1.1.10
  • chemical-elements ^1.2.3
  • chemical-groups ^1.2.1
packages/mf-utilities/package.json npm
  • chemical-elements ^1.2.3
  • chemical-groups ^1.2.1
  • mf-parser ^1.4.7
packages/ms-report/package.json npm
  • @svgdotjs/svg.js 3.1.1
  • chemical-groups ^1.2.1
  • mf-utilities ^1.3.3
  • nucleotide ^1.2.21
  • peptide ^1.11.4
  • svgdom 0.0.21
packages/ms-spectrum/package.json npm
  • jest-matcher-deep-close-to ^3.0.2 development
  • spectrum-generator ^8.0.1 development
  • emdb ^1.10.2
  • is-any-array ^2.0.0
  • mf-parser ^1.4.7
  • ml-array-max ^1.2.4
  • ml-array-min ^1.2.3
  • ml-array-normed ^1.3.7
  • ml-gsd ^10.2.0
  • ml-regression-power ^2.0.0
  • ml-spectra-processing ^11.1.0
  • peaks-similarity ^2.3.1
  • xy-parser ^5.0.2
.github/workflows/documentationjs.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/lactame.yml actions
  • actions/checkout v2 composite
  • actions/setup-node v3 composite
  • zakodium/lactame-action v1 composite
.github/workflows/release.yml actions
  • actions/checkout v2 composite
  • actions/setup-node v3 composite
  • google-github-actions/release-please-action v3 composite
packages/mass-fragmentation/package.json npm
  • openchemlib ^8.0.1 development
  • mf-parser ^2.1.0
  • openchemlib-utils ^2.1.2
.github/workflows/nodejs.yml actions
packages/atom-sorter/package.json npm
packages/chemical-groups/package.json npm
packages/mfs-deconvolution/package.json npm
  • fifo-logger ^0.6.1 development
  • xy-parser ^5.0.4 development
  • cheminfo-types ^1.7.2
  • isotopic-distribution ^3.0.1
  • mf-generator ^3.0.1
  • ml-fcnnls ^2.1.0
  • ml-matrix ^6.10.4
  • ml-spectra-processing ^12.5.0
  • ms-spectrum ^3.0.1