Science Score: 51.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
2 of 10 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.6%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
just annotate it, dammit!
Basic Info
- Host: GitHub
- Owner: dib-lab
- License: other
- Language: Python
- Default Branch: master
- Homepage: http://dib-lab.github.io/dammit/
- Size: 12.1 MB
Statistics
- Stars: 93
- Watchers: 12
- Forks: 28
- Open Issues: 79
- Releases: 0
Topics
Metadata Files
README.md
"I love writing BLAST parsers!" -- no one, ever
dammit is a simple de novo transcriptome annotator. It was born out of the observation that: annotation is mundane and annoying; all the individual pieces of the process exist already; and, the existing solutions are overly complicated or rely on crappy non-free software.
Science shouldn't suck for the sake of sucking, so dammit attempts to make this sucky part of the process suck a little less.
Basic Usage
Install dammit with bioconda.
conda create -n dammit-env python=3 dammit
conda activate dammit-env
Download and install a subset of the databases:
dammit databases --install --quick
And the annotate with:
dammit annotate <transcriptome_fasta>
Head over to the docs for much more detailed information!
Acknowledgements
I've received input and advice from a many sources, including but probably not limited to: C Titus Brown, Matt MacManes, Chris Hamm, Michael Crusoe, Russell Neches, Luiz Irber, Lisa Cohen, Tessa Pierce, Sherine Awad, and Tamer Mansour.
CS was funded by the National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG007513 through May 2016, and now receives support from the Gordon and Betty Moore Foundation under Award number GBMF4551.
Owner
- Name: The Lab for Data Intensive Biology
- Login: dib-lab
- Kind: organization
- Location: University of California, Davis, School of Veterinary Medicine, Davis, California, USA
- Website: http://ivory.idyll.org/lab/
- Repositories: 104
- Profile: https://github.com/dib-lab
Previously "Genomics, Evolution, and Development Lab" @ Michigan State University
Citation (CITATION)
@article{scott_dammit_2016,
title = {dammit: an open and accessible de novo transcriptome annotator},
url = {www.camillescott.org/dammit},
journal = {in prep.},
author = {Scott, Camille},
year = {2016}
}
GitHub Events
Total
- Watch event: 5
Last Year
- Watch event: 5
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Camille Scott | c****w@g****m | 563 |
| Tessa Pierce | n****e@g****m | 35 |
| Lisa K. Johnson | l****n@u****u | 21 |
| C. Titus Brown | t****s@i****g | 8 |
| Tessa Pierce | b****s | 8 |
| C Reid | c****1@G****m | 5 |
| Luiz Irber | l****r@g****m | 1 |
| Chris Hamm | c****m@k****u | 1 |
| dependabot[bot] | 4****] | 1 |
| The Gitter Badger | b****r@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 57
- Total pull requests: 46
- Average time to close issues: 6 months
- Average time to close pull requests: 3 months
- Total issue authors: 36
- Total pull request authors: 8
- Average comments per issue: 1.54
- Average comments per pull request: 0.22
- Merged pull requests: 30
- 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
Top Authors
Issue Authors
- camillescott (11)
- bluegenes (8)
- johnsolk (2)
- DrPintoThe2nd (2)
- christa88 (2)
- incoreygible (2)
- ppericard (1)
- macmanes (1)
- mictadlo (1)
- jarcasariego (1)
- CeciliaDeng (1)
- shrhops (1)
- eburgueno (1)
- sformel (1)
- ncnlll (1)
Pull Request Authors
- camillescott (26)
- bluegenes (12)
- taylorreiter (2)
- luizirber (2)
- NickCrews (1)
- rix133 (1)
- eburgueno (1)
- pansapiens (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- Sphinx >=1.3.1
- doit *
- setuptools >=0.6.35
- sphinx-rtd-theme >=0.1.9
- Sphinx >1.3.1
- doit ==0.29.0
- ficus >=0.1
- filelock *
- khmer >=2.0
- matplotlib >=1.0
- numexpr >=2.3.1
- pandas >=0.18.1
- pytest >3
- pytest-cov >2.3
- setuptools >=0.6.35
- sh *
- shmlast >=1.2
- sphinx-rtd-theme >=0.1.9
- sphinxcontrib-napoleon >=0.3.11
- doit >=0.29.0
- ficus >=0.1
- filelock *
- khmer >=2.0
- matplotlib >=1.0
- numexpr >=2.3.1
- pandas >=0.18.1
- setuptools >=0.6.35
- sh *
- shmlast >=1.2