atlas
Single-file quality control prototyping pipeline for diverse mass spectrometry workflows.
Science Score: 26.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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○Scientific vocabulary similarity
Low similarity (8.4%) to scientific vocabulary
Keywords
Repository
Single-file quality control prototyping pipeline for diverse mass spectrometry workflows.
Basic Info
- Host: GitHub
- Owner: proteomicsunitcrg
- License: other
- Language: Nextflow
- Default Branch: main
- Homepage: https://demo-qsample.crg.eu
- Size: 191 MB
Statistics
- Stars: 1
- Watchers: 4
- Forks: 0
- Open Issues: 8
- Releases: 13
Topics
Metadata Files
README.md
Atlas
Introduction
Atlas is a Nextflow-based pipeline developed for the processing and analysis of mass spectrometry data, specifically designed to assist proteomics laboratories with daily quality assessments across various proteomics applications. It supports multiple workflows, such as regular proteomes, phosphoproteomes, and independent acquisition modes, among others.
With these diverse workflows, Atlas extracts critical quality control parameters, simplifying the evaluation of mass spectrometry experiments. Atlas can be configured to use various search engines, including:
The pipeline is implemented using the latest Nextflow DSL2 syntax and is designed to operate efficiently in HPC (High-Performance Computing) environments.
For more detailed information, please refer to the documentation.
Credits
The Atlas pipeline was initially developed by @rolivella.
We would like to express our gratitude to the following individuals for their valuable contributions during the development:
- Eduard Sabid (@edunivers)
- Cristina Chiva
- Eva Borrs
- Guadalupe Espadas
- Olga Pastor
- Enrique Alonso
- Selena Fernndez
Citations
A comprehensive list of references for the tools utilized in the pipeline can be found in the CITATIONS.md file.
Owner
- Name: CRG/UPF Protemics Unit
- Login: proteomicsunitcrg
- Kind: organization
- Location: Barcelona
- Repositories: 11
- Profile: https://github.com/proteomicsunitcrg
GitHub Events
Total
- Create event: 3
- Release event: 2
- Issues event: 19
- Issue comment event: 53
- Push event: 39
- Public event: 1
- Gollum event: 29
- Pull request event: 16
Last Year
- Create event: 3
- Release event: 2
- Issues event: 19
- Issue comment event: 53
- Push event: 39
- Public event: 1
- Gollum event: 29
- Pull request event: 16
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 12
- Total pull requests: 10
- Average time to close issues: 4 months
- Average time to close pull requests: 30 minutes
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 5.33
- Average comments per pull request: 0.0
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 10
- Pull requests: 10
- Average time to close issues: 27 days
- Average time to close pull requests: 30 minutes
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.5
- Average comments per pull request: 0.0
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- rolivella (12)
Pull Request Authors
- rolivella (10)