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https://github.com/cheminfo/dereplication

Computing similarity between experimental and predicted mass spectra.

https://github.com/cheminfo/dereplication

Science Score: 13.0%

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    Low similarity (10.6%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Computing similarity between experimental and predicted mass spectra.

Basic Info
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 0
  • Open Issues: 2
  • Releases: 0
Created about 6 years ago · Last pushed about 6 years ago
Metadata Files
Readme License

README.md

dereplication

NPM version build status npm download

Handling large JSON files with experimental and predicted mass spectra. Computing similarity between an experiment and a predicted spectrum and finding best match.

Installation

$ npm i dereplication

Usage

The code underneath allows you to have a lot of information about the similarity results between experiments and predictions. To see the debug information, use this command: bash DEBUG=testSimilarity node --max-old-space-size=8192 -r esm index.js

The --max-old-space-size=8192 option has to be used because Node.js cannot handle files this large otherwise.

The code underneath should be the contents of index.js.

```js import { similarity as Similarity } from 'ml-distance';

import computeSimilarities from './computeSimilarities';

const intersection = Similarity.intersection;

const experimental = './data/matchingExperiments.json'; const predicted = './data/predictions.json';

computeSimilarities(experimental, predicted, { numExperiments: undefined, bestMatch: { massFilter: 0.05, }, loadData: { numberMaxPeaks: undefined, mergeSpan: 0.05, norm: true, }, similarity: { alignDelta: 0.05, algorithm: intersection, norm: false, }, }); ```

API Documentation

CLick on this link to access the API documentation.

Project documentation and results

License

MIT

Owner

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

GitHub Events

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Last Year

Issues and Pull Requests

Last synced: about 1 year ago

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  • Total issues: 8
  • Total pull requests: 0
  • Average time to close issues: 6 days
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 1.25
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • lpatiny (7)
  • opatiny (1)
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Dependencies

.github/workflows/nodejs.yml actions
  • actions/checkout v2 composite
  • actions/setup-node v1 composite
package.json npm
  • @babel/plugin-transform-modules-commonjs ^7.9.0 development
  • @types/jest ^25.2.1 development
  • debug ^4.1.1 development
  • eslint ^6.8.0 development
  • eslint-config-cheminfo ^3.0.0 development
  • eslint-plugin-import ^2.20.2 development
  • eslint-plugin-jest ^23.8.2 development
  • eslint-plugin-prettier ^3.1.3 development
  • jest ^25.3.0 development
  • ml-array-sum ^1.1.2 development
  • prettier ^2.0.4 development
  • rollup ^2.6.1 development
  • mgf-parser ^0.2.1
  • ml-array-max ^1.1.2
  • ml-array-mean ^1.1.2
  • ml-array-median ^1.1.3
  • ml-array-min ^1.1.2
  • ml-array-normed ^1.2.0
  • ml-array-xy-weighted-merge ^1.0.1
  • ml-distance ^3.0.0
  • ml-spectra-processing ^2.2.0
  • openchemlib ^7.2.3
  • papaparse ^5.2.0