https://github.com/alexandrovlab/sigprofilerextractor
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
https://github.com/alexandrovlab/sigprofilerextractor
Keywords
bioinformatics cancer-genomics mutation-analysis mutational-signatures somatic-variants
Last synced: 11 months ago
JSON representation
Acceptance Criteria
- Revelant topics? true
- External users? true
- Open source license? true
- Active? true
- Fork? false
Repository metadata
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
- Host: GitHub
- URL: https://github.com/alexandrovlab/sigprofilerextractor
- Owner: AlexandrovLab
- License: bsd-2-clause
- Created: 2018-08-30T23:23:09.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2024-05-10T17:54:28.000Z (12 months ago)
- Last Synced: 2024-05-15T00:00:08.480Z (12 months ago)
- Topics: bioinformatics, cancer-genomics, mutation-analysis, mutational-signatures, somatic-variants
- Language: Python
- Homepage:
- Size: 166 MB
- Stars: 146
- Watchers: 23
- Forks: 51
- Open Issues: 5
- Releases: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Owner metadata
- Name: Alexandrov Lab
- Login: AlexandrovLab
- Email: [email protected]
- Kind: organization
- Description:
- Website: http://alexandrov.ucsd.edu/
- Location: La Jolla, CA
- Twitter:
- Company:
- Icon url: https://avatars.githubusercontent.com/u/42589306?v=4
- Repositories: 12
- Last ynced at: 2023-03-02T21:10:39.910Z
- Profile URL: https://github.com/AlexandrovLab
GitHub Events
Total
- Fork event: 51
- Create event: 81
- Commit comment event: 1
- Release event: 3
- Issues event: 342
- Watch event: 145
- Delete event: 57
- Member event: 4
- Issue comment event: 502
- Push event: 321
- Public event: 1
- Pull request review event: 2
- Pull request event: 92
Last Year
- Create event: 23
- Delete event: 19
- Fork event: 9
- Issue comment event: 63
- Issues event: 66
- Pull request event: 6
- Push event: 14
- Release event: 1
- Watch event: 22
Committers metadata
Last synced: over 1 year ago
Total Commits: 387
Total Committers: 9
Avg Commits per committer: 43.0
Development Distribution Score (DDS): 0.393
Commits in past year: 7
Committers in past year: 1
Avg Commits per committer in past year: 7.0
Development Distribution Score (DDS) in past year: 0.0
| Name | Commits | |
|---|---|---|
| mishu | m****1@h****m | 235 |
| mdbarnesUCSD | m****s@u****u | 81 |
| Raviteja Vangara | r****a@g****m | 30 |
| Marcos Díaz-Gay | m****y@u****u | 19 |
| Mike Vella | m****a@n****m | 10 |
| Octocoot | h****u@g****m | 9 |
| David A. Parry | d****y@e****k | 1 |
| mdbarnesUCSD | m****s@h****u | 1 |
| Ludmil Alexandrov | 4****8 | 1 |
Committer domains:
- ucsd.edu: 2
- health.ucsd.edu: 1
- ed.ac.uk: 1
- nvidia.com: 1
Issue and Pull Request metadata
Last synced: 12 months ago
Total issues: 124
Total pull requests: 33
Average time to close issues: 9 days
Average time to close pull requests: 1 day
Total issue authors: 84
Total pull request authors: 5
Average comments per issue: 2.31
Average comments per pull request: 0.09
Merged pull request: 31
Bot issues: 0
Bot pull requests: 0
Past year issues: 54
Past year pull requests: 3
Past year average time to close issues: 8 days
Past year average time to close pull requests: 5 days
Past year issue authors: 29
Past year pull request authors: 1
Past year average comments per issue: 2.26
Past year average comments per pull request: 0.0
Past year merged pull request: 3
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- KANGseungseok (6)
- JLiandbear (5)
- me-nobody (5)
- sainadfensi (5)
- anderdnavarro (4)
- xiaoyaojianghuzai (4)
- daanhazelaar (4)
- oliverartz (2)
- pushpa-itagi (2)
- rsg344 (2)
- RTCarmo (2)
- ruinw (2)
- shenhaizhongdechanrao (2)
- nash5202 (2)
- nan5895 (2)
Top Pull Request Authors
- mdbarnesUCSD (19)
- rvangara (6)
- marcos-diazg (6)
- nithishbn (1)
- david-a-parry (1)
Top Issue Labels
- enhancement (2)
- good first issue (2)
- bug (1)
Top Pull Request Labels
Package metadata
- Total packages: 4
-
Total downloads:
- pypi: 2,009 last-month
- Total docker downloads: 670
- Total dependent packages: 1 (may contain duplicates)
- Total dependent repositories: 4 (may contain duplicates)
- Total versions: 158
- Total maintainers: 4
pypi.org: sigprofilerextractor
Extracts mutational signatures from mutational catalogues
- Homepage: https://github.com/AlexandrovLab/SigProfilerExtractor.git
- Documentation: https://sigprofilerextractor.readthedocs.io/
- Licenses: UCSD
- Latest release: 1.1.24 (published 12 months ago)
- Last Synced: 2024-05-14T19:19:59.972Z (12 months ago)
- Versions: 51
- Dependent Packages: 1
- Dependent Repositories: 1
- Downloads: 1,131 Last month
-
Rankings:
- Dependent packages count: 4.728%
- Downloads: 5.963%
- Forks count: 5.965%
- Stargazers count: 6.189%
- Average: 8.91%
- Dependent repos count: 21.705%
- Maintainers (3)
pypi.org: sigproextractor
Extracts mutational signatures from mutational catalogues
- Homepage: https://github.com/AlexandrovLab/SigProfilerExtractor.git
- Documentation: https://sigproextractor.readthedocs.io/
- Licenses: UCSD
- Latest release: 0.0.5 (published over 6 years ago)
- Last Synced: 2024-05-15T09:28:52.747Z (12 months ago)
- Versions: 79
- Dependent Packages: 0
- Dependent Repositories: 1
- Downloads: 568 Last month
- Docker Downloads: 670
-
Rankings:
- Docker downloads count: 2.457%
- Forks count: 5.967%
- Stargazers count: 6.19%
- Dependent packages count: 10.002%
- Average: 10.234%
- Downloads: 15.067%
- Dependent repos count: 21.718%
- Maintainers (1)
pypi.org: sigpross
Decomposes mutational catalogues to mutational signatures
- Homepage: https://github.com/AlexandrovLab/SigProfilerExtractor.git
- Documentation: https://sigpross.readthedocs.io/
- Licenses: UCSD
- Latest release: 0.0.0.27 (published almost 5 years ago)
- Last Synced: 2024-05-15T09:28:52.764Z (12 months ago)
- Versions: 27
- Dependent Packages: 0
- Dependent Repositories: 1
- Downloads: 293 Last month
-
Rankings:
- Forks count: 5.967%
- Stargazers count: 6.19%
- Dependent packages count: 10.002%
- Average: 12.902%
- Downloads: 20.633%
- Dependent repos count: 21.718%
- Maintainers (3)
pypi.org: new-sigproextractor
Extracts mutational signatures from mutational catalogues
- Homepage: https://github.com/AlexandrovLab/SigProfilerExtractor.git
- Documentation: https://new-sigproextractor.readthedocs.io/
- Licenses: UCSD
- Latest release: 0.0.0.1 (published almost 6 years ago)
- Last Synced: 2024-05-15T09:28:52.702Z (12 months ago)
- Versions: 1
- Dependent Packages: 0
- Dependent Repositories: 1
- Downloads: 17 Last month
-
Rankings:
- Forks count: 5.967%
- Stargazers count: 6.19%
- Dependent packages count: 10.002%
- Average: 17.888%
- Dependent repos count: 21.718%
- Downloads: 45.564%
- Maintainers (1)
Dependencies
Score: 15.111429070420009