Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com, zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.6%) to scientific vocabulary
Keywords
Repository
BugSigDB data files
Statistics
- Stars: 3
- Watchers: 2
- Forks: 4
- Open Issues: 3
- Releases: 16
Topics
Metadata Files
README.md
Hourly export status: 
BugSigDBExports
This repository contains data files exported from BugSigDB, a manually curated database of published microbial signatures.
See https://doi.org/10.5281/zenodo.5606165 for all releases.
Citation
Ludwig Geistlinger, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Clare Grieve, Jennifer Wokaty, Samuel David Gamboa-Tuz, Pratyay Sengupta, Isaac Hecht, Aarthi Ravikrishnan, Rafael Goncalves, Eric Franzosa, Karthik Raman, Vincent Carey, Jennifer B. Dowd, Heidi E. Jones, Sean Davis, Nicola Segata, Curtis Huttenhower, Levi Waldron (2023) BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures. Nature Biotechnology, doi: 10.1038/s41587-023-01872-y.
What does BugSigDBExports do?
At the core of the repo is the dump_release.R script which
- obtains and merges the exported study, experiment, and signature tables from https://bugsigdb.org/Help:Export,
- filters incomplete records,
- adds signature IDs,
- writes the full dump to csv, and
- writes GMT files of signatures for all combinations of ID type and taxonomic level.
This script is invoked automatically every hour via a cron job.
bugsigdb-related links
- bugsigdb.org: A Comprehensive Database of Published Microbial Signatures
- BugSigDB issue tracker: Report bugs or feature requests for bugsigdb.org
- BugSigDBExports: Hourly data exports of bugsigdb.org
- Stable data releases: Periodic manually-reviewed stable data releses on Zenodo
- bugsigdbr: R/Bioconductor access to published microbial signatures from BugSigDB
- Curation issues: Report curation issues, requests studies to be added
- bugSigSimple: Simple analyses of BugSigDB data in R
- BugSigDBStats: Statistics and trends of BugSigDB
- BugSigDBPaper: Reproduces analyses of the Nature Biotechnology publication
- community-bioc Slack Team: Join #bugsigdb channel
Owner
- Name: Waldron Lab at the CUNY SPH
- Login: waldronlab
- Kind: organization
- Email: Levi.Waldron@sph.cuny.edu
- Location: New York, NY, USA
- Website: https://waldronlab.io/
- Twitter: LeviWaldron1
- Repositories: 93
- Profile: https://github.com/waldronlab
Software and educational materials from the Waldron lab for computational biostatistics at the CUNY SPH in New York City
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 8
- Total pull requests: 3
- Average time to close issues: 11 months
- Average time to close pull requests: 4 days
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 2.38
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 3
- Average time to close issues: 20 days
- Average time to close pull requests: 4 days
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jwokaty (6)
- cmirzayi (3)
- sdgamboa (2)
- lwaldron (1)
Pull Request Authors
- jwokaty (3)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite