https://github.com/alondmnt/codon-bias
Python package of codon usage bias analysis tools
Science Score: 13.0%
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
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○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.7%) to scientific vocabulary
Keywords
Repository
Python package of codon usage bias analysis tools
Basic Info
- Host: GitHub
- Owner: alondmnt
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://codon-bias.readthedocs.io
- Size: 203 KB
Statistics
- Stars: 17
- Watchers: 1
- Forks: 8
- Open Issues: 0
- Releases: 5
Topics
Metadata Files
README.md
codon-bias
This package provides codon usage bias (CUB) analysis tools for genomic sequences, focusing on protein coding regions, translation efficiency and synonymous mutations. These include implementations of popular models from the past four decades of codon usage study, such as:
- Nucleotide and codon k-mer statistics (GC, GC3, CpG, etc.)
- Frequency of Optimal Codons (FOP)
- Relative Synonymous Codon Usage (RSCU)
- Codon Adaptation Index (CAI), including extensions:
- Codon pair (and k-mers) adaptation
- Effective Number of Codons (ENC), including extensions:
- Background correction
- Improved estimation
- Effective number of codon pairs (and k-mers) (ENcp)
- tRNA Adaptation Index (tAI)
- Download tRNA gene copy numbers from GtRNAdb
- Train tAI model parameters (s-values) using expression levels
- Codon Pair Bias (CPB/CPS)
- Relative Codon Bias Score (RCBS)
- Normalized Translational Efficiency (nTE)
- Directional Codon Bias Score (DCBS)
- Codon Usage Frequency Similarity (CUFS)
This package also includes tools for sequence optimization based on these codon usage models, and generators of random sequence permutations that can be used to compute empirical p-values and z-scores.
installation
pip install codon-bias
documentation
Read on Read the Docs.
cite
Diament, A. (2022). codon-bias (python package). https://doi.org/10.5281/zenodo.8039451
contributing
Contributions of additional models to the package are welcome! Please familiarize yourself with the existing classes, and try to conform to their style.
Owner
- Name: Alon Diament Carmel
- Login: alondmnt
- Kind: user
- Company: @PhenoAI
- Website: alondmnt.com
- Repositories: 26
- Profile: https://github.com/alondmnt
computational biologist & data scientist, PhD
GitHub Events
Total
- Create event: 3
- Issues event: 2
- Release event: 3
- Watch event: 9
- Issue comment event: 18
- Push event: 16
- Pull request event: 3
- Pull request review event: 3
- Fork event: 3
Last Year
- Create event: 3
- Issues event: 2
- Release event: 3
- Watch event: 9
- Issue comment event: 18
- Push event: 16
- Pull request event: 3
- Pull request review event: 3
- Fork event: 3
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 85
- Total Committers: 1
- Avg Commits per committer: 85.0
- Development Distribution Score (DDS): 0.0
Top Committers
| Name | Commits | |
|---|---|---|
| Alon Diament | a****t@u****m | 85 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 3
- Total pull requests: 3
- Average time to close issues: 3 days
- Average time to close pull requests: 12 days
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 1.0
- Average comments per pull request: 2.33
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 3
- Average time to close issues: about 20 hours
- Average time to close pull requests: 12 days
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 2.33
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- zihian (1)
- deyuanyang (1)
- ShlozLavie (1)
Pull Request Authors
- l-benedetti-insta (2)
- moritzburghardt (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 2,530 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 8
- Total maintainers: 1
pypi.org: codon-bias
codon usage bias analysis tools
- Homepage: https://github.com/alondmnt/codon-bias
- Documentation: https://codon-bias.readthedocs.io/en/latest/
- License: MIT
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Latest release: 0.3.5
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- numpy *
- pandas *
- scipy *