Science Score: 59.0%
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 3 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
✓Committers with academic emails
8 of 17 committers (47.1%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.8%) to scientific vocabulary
Keywords from Contributors
Repository
Bioinformatics program inStrain
Basic Info
- Host: GitHub
- Owner: MrOlm
- License: mit
- Language: Python
- Default Branch: master
- Size: 261 MB
Statistics
- Stars: 168
- Watchers: 6
- Forks: 36
- Open Issues: 12
- Releases: 1
Metadata Files
README.md
inStrain
inStrain is a python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification.
Manual, installation instructions, and expected output are at available at ReadTheDocs
Publication is available in Nature Biotechnology and on bioRxiv
Installation options
pip
$ pip install instrain
bioconda
$ conda install -c conda-forge -c bioconda -c defaults instrain
Docker
Docker image is available on Docker Hub at mattolm/instrain. See docker/ for use instructions.
Quick start
Show program help and modules:
$ inStrain -h
Microdiversity and SNP-calling pipeline:
$ inStrain profile mapping.bam genome_file.fasta -o inStrain_profile1
Detailed strain-level comparison:
$ inStrain compare inStrain_profile1 inStrain_profile2
Owner
- Name: Matt Olm
- Login: MrOlm
- Kind: user
- Location: San Francisco, CA
- Company: Stanford University
- Website: https://mrolm.github.io/
- Twitter: MattagenOlmics
- Repositories: 8
- Profile: https://github.com/MrOlm
Postdoc in Justin Sonnenburg's lab at Stanford
GitHub Events
Total
- Issues event: 55
- Watch event: 31
- Issue comment event: 57
- Push event: 5
- Fork event: 3
- Create event: 1
Last Year
- Issues event: 55
- Watch event: 31
- Issue comment event: 57
- Push event: 5
- Fork event: 3
- Create event: 1
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Matt Olm | m****m@g****m | 157 |
| Matt Olm | m****m@M****l | 54 |
| Alex Crits-Christoph | a****1@j****u | 18 |
| Matt Olm | m****m@M****l | 15 |
| Matt Olm | m****m@M****l | 11 |
| Matt Olm | m****m@s****u | 3 |
| Matt Olm | m****m@m****u | 3 |
| Jing Wang | z****e@s****n | 2 |
| Matt Olm | m****m@D****t | 2 |
| Matt Olm | m****m@b****u | 1 |
| Matt Olm | m****m@s****u | 1 |
| Matt Olm | m****m@u****u | 1 |
| szimmerman92 | s****n@g****m | 1 |
| rusher321 | r****i@g****n | 1 |
| Vini Salazar | 1****r | 1 |
| Mike Lee | m****7@g****m | 1 |
| Francisco Zorrilla | f****4@c****k | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 155
- Total pull requests: 7
- Average time to close issues: 2 months
- Average time to close pull requests: 1 day
- Total issue authors: 99
- Total pull request authors: 7
- Average comments per issue: 3.69
- Average comments per pull request: 1.43
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 21
- Pull requests: 0
- Average time to close issues: 19 days
- Average time to close pull requests: N/A
- Issue authors: 18
- Pull request authors: 0
- Average comments per issue: 1.29
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- gabrieleghiotto (5)
- ChenTianYi99 (5)
- liamfitzstevens (5)
- haihao999 (4)
- jmartin77777 (4)
- zhaoc1 (4)
- mcmahon-uw (3)
- jdwinkler-lanzatech (3)
- kirkgrubbs1 (3)
- rrohwer (3)
- 473021677 (3)
- rebeccasophiasalcedo (3)
- Thexiyang (3)
- DDavila10 (3)
- szimmerman92 (2)
Pull Request Authors
- zhenjiaofenjie (2)
- alexcritschristoph (1)
- nick-youngblut (1)
- rusher321 (1)
- vinisalazar (1)
- szimmerman92 (1)
- franciscozorrilla (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 56 last-month
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 65
- Total maintainers: 2
pypi.org: instrain
Calculation of strain-level metrics
- Homepage: https://github.com/MrOlm/inStrain
- Documentation: https://instrain.readthedocs.io/
- License: MIT
-
Latest release: 1.10.0
published 10 months ago
Rankings
Maintainers (1)
spack.io: py-instrain
inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non- synonymous identification.
- Homepage: https://github.com/MrOlm/instrain
- License: []
-
Latest release: 1.6.3
published about 3 years ago
Rankings
Maintainers (1)
Dependencies
- biopython <=1.74
- h5py *
- lmfit *
- matplotlib *
- networkx *
- numba *
- numpy *
- pandas >=0.25,
- psutil *
- pysam >=0.15
- pytest *
- scikit-learn *
- seaborn *
- tqdm *
- continuumio/miniconda3 4.6.14 build
- continuumio/miniconda3 latest build