soprano
SelectiOn in PRotein ANnotated regiOns. Adapted dN/dS based method to detect selection in specific protein regions
Science Score: 36.0%
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○Scientific vocabulary similarity
Low similarity (8.5%) to scientific vocabulary
Repository
SelectiOn in PRotein ANnotated regiOns. Adapted dN/dS based method to detect selection in specific protein regions
Basic Info
- Host: GitHub
- Owner: instituteofcancerresearch
- License: gpl-3.0
- Language: Python
- Default Branch: python
- Homepage: https://instituteofcancerresearch.github.io/SOPRANO/
- Size: 125 MB
Statistics
- Stars: 3
- Watchers: 0
- Forks: 0
- Open Issues: 13
- Releases: 2
Metadata Files
README.md
SOPRANO
Selection On PRotein ANnotated regiOns
This can be accessed via the webserver: soprano-app
The SOPRANO method was developed to quantify selection in specific regions of the genome. It calculates ON- and OFF-target dN/dS using a set of annotated somatic point mutations and a transcript coordinates file.
This repository is a Python reimplementation of the original method with two main offerings:
- An application interface to easily pre-process the relevant input files.
- A scalable command line utility to run the SOPRANO pipeline for dN/dS, serving local and high-performance computing environments, distributed over MPI.
Quick links
Documentation is available on this site.
Issues should be raised here.
Reference the SOPRANO method with Zapata et al.
View the original repository here.
Owner
- Name: The Institute of Cancer Research
- Login: instituteofcancerresearch
- Kind: organization
- Location: United Kingdom
- Website: https://www.icr.ac.uk/
- Twitter: ICR_London
- Repositories: 30
- Profile: https://github.com/instituteofcancerresearch
Making the discoveries that defeat cancer.
GitHub Events
Total
- Issues event: 6
- Issue comment event: 3
- Push event: 13
- Pull request review event: 1
- Pull request event: 4
- Create event: 2
Last Year
- Issues event: 6
- Issue comment event: 3
- Push event: 13
- Pull request review event: 1
- Pull request event: 4
- Create event: 2
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 1
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- bkmarzouk (11)
- rachelicr (3)
- faizjab (2)
- LongpanUPC (1)
- Y-u-q-i (1)
- myy1823 (1)
- msarkis-icr (1)
Pull Request Authors
- bkmarzouk (20)
- rachelicr (9)
- msarkis-icr (1)
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Dependencies
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- actions/checkout v3 composite
- actions/setup-python v4 composite
- condaforge/mambaforge 23.3.1-1 build
- actions/cache v3 composite
- actions/checkout v4 composite
- actions/setup-python v4 composite