cpg-gnomad
Hail helper functions for the gnomAD project and Translational Genomics Group
Science Score: 36.0%
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
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○Academic publication links
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✓Committers with academic emails
13 of 27 committers (48.1%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.6%) to scientific vocabulary
Keywords
exomes
genomes
genomics
hail
Keywords from Contributors
bioinformatics
genetics
gwas
software
vcf
interactive
serializer
packaging
network-simulation
shellcodes
Last synced: 6 months ago
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JSON representation
Repository
Hail helper functions for the gnomAD project and Translational Genomics Group
Basic Info
- Host: GitHub
- Owner: broadinstitute
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://gnomad.broadinstitute.org
- Size: 6.46 MB
Statistics
- Stars: 96
- Watchers: 24
- Forks: 30
- Open Issues: 18
- Releases: 15
Topics
exomes
genomes
genomics
hail
Created over 8 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
Contributing
License
Codeowners
README.md
Hail utilities for gnomAD
This repo contains a number of Hail utility functions and scripts for the gnomAD project and the Translational Genomics Group. As we continue to expand the size of our datasets, we are constantly seeking to find ways to reduce the complexity of our workflows and to make these functions more generic. As a result, the interface for many of these functions will change over time as we generalize their implementation for more flexible use within our scripts. We are also continously adapting our code to regular changes in the Hail interface. These repos thus represent only a snapshot of the gnomAD code base and are shared without guarantees or warranties.
We therefore encourage users to browse through the API reference to identify modules and functions that will be useful in their own pipelines, and to edit and reconfigure relevant code to suit their particular analysis and QC needs.
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
GitHub Events
Total
- Fork event: 2
- Create event: 44
- Commit comment event: 1
- Release event: 1
- Issues event: 25
- Watch event: 10
- Delete event: 40
- Issue comment event: 46
- Member event: 1
- Push event: 339
- Pull request event: 79
- Pull request review event: 269
- Pull request review comment event: 361
Last Year
- Fork event: 2
- Create event: 44
- Commit comment event: 1
- Release event: 1
- Issues event: 25
- Watch event: 10
- Delete event: 40
- Issue comment event: 46
- Member event: 1
- Push event: 339
- Pull request event: 79
- Pull request review event: 269
- Pull request review comment event: 361
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| jkgoodrich | j****c@b****g | 707 |
| Qin He | 4****n | 397 |
| Mike Wilson | m****n@b****g | 339 |
| klaricch | k****n@b****g | 326 |
| Katherine Chao | k****o@b****g | 262 |
| konradjk | k****i@g****m | 225 |
| laurent | l****n@b****g | 197 |
| Nick Watts | n****s@b****g | 109 |
| gtiao | g****o@b****g | 77 |
| Kyle Ferriter | k****e@b****g | 39 |
| averywpx | a****x@g****m | 32 |
| wlu04 | w****4 | 29 |
| Daniel Marten | m****n@b****g | 26 |
| wphu | w****2@g****m | 23 |
| dependabot[bot] | 4****] | 12 |
| averywpx | 5****x | 7 |
| Masahiro Kanai | m****i@b****g | 2 |
| Besse Cummings | b****c@b****g | 2 |
| Daniel King | d****g@b****g | 2 |
| Tim Poterba | t****a@g****m | 1 |
| Rayna M Harris | r****s | 1 |
| QingboWang | Q****g | 1 |
| Matthew Solomonson | g****t@g****m | 1 |
| Konrad Karczewski | k****k@b****g | 1 |
| John Marshall | j****l@p****u | 1 |
| Konrad Karczewski | k****k@K****l | 1 |
| Chris Vittal | c****s@v****v | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 68
- Total pull requests: 307
- Average time to close issues: 12 months
- Average time to close pull requests: 12 days
- Total issue authors: 21
- Total pull request authors: 16
- Average comments per issue: 1.63
- Average comments per pull request: 0.57
- Merged pull requests: 257
- Bot issues: 0
- Bot pull requests: 16
Past Year
- Issues: 13
- Pull requests: 74
- Average time to close issues: 13 days
- Average time to close pull requests: 11 days
- Issue authors: 4
- Pull request authors: 8
- Average comments per issue: 1.15
- Average comments per pull request: 0.38
- Merged pull requests: 61
- Bot issues: 0
- Bot pull requests: 4
Top Authors
Issue Authors
- matren395 (16)
- jkgoodrich (10)
- mike-w-wilson (8)
- ch-kr (7)
- nawatts (7)
- klaricch (3)
- averywpx (2)
- KoalaQin (2)
- gtiao (2)
- LindoNkambule (1)
- xsun1229 (1)
- Jingning-Zhang (1)
- PoisonAlien (1)
- Ruchit10 (1)
- smhaider (1)
Pull Request Authors
- jkgoodrich (129)
- KoalaQin (66)
- mike-w-wilson (54)
- klaricch (52)
- dependabot[bot] (22)
- ch-kr (15)
- matren395 (10)
- averywpx (7)
- theferrit32 (6)
- konradjk (2)
- tpoterba (1)
- LindoNkambule (1)
- jmarshall (1)
- Ruchit10 (1)
- mkanai (1)
Top Labels
Issue Labels
Needs Refinement (5)
Epic (4)
Frequency (2)
Unplanned (2)
enhancement (2)
v4 (2)
v5 (2)
Sample QC (1)
bug (1)
annotation (1)
Changelog: new feature (1)
Pull Request Labels
Changelog: new feature (139)
Changelog: ignore (78)
Changelog: bug fix (32)
dependencies (25)
Changelog: breaking change (20)
Frequency (17)
Pext (17)
v4 (16)
Unplanned (13)
Coverage (10)
v4.1 (9)
Constraint (9)
Resources (7)
annotation (7)
ga4gh VRS (7)
bug (7)
Variant QC annotation (6)
Variant QC (6)
Sample QC (4)
python (4)
VCF (3)
Release Stats (3)
v5 (3)
Sample outlier filter (2)
Relatedness (2)
Packages
- Total packages: 2
-
Total downloads:
- pypi 1,763 last-month
- Total docker downloads: 104,255
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 2
(may contain duplicates) - Total versions: 22
- Total maintainers: 4
pypi.org: gnomad
Hail utilities for the Genome Aggregation Database
- Homepage: https://github.com/broadinstitute/gnomad_methods
- Documentation: https://broadinstitute.github.io/gnomad_methods/
- License: MIT License
-
Latest release: 0.8.2
published about 1 year ago
Rankings
Docker downloads count: 1.1%
Forks count: 7.7%
Stargazers count: 8.0%
Downloads: 9.0%
Average: 9.6%
Dependent packages count: 10.1%
Dependent repos count: 21.6%
Last synced:
6 months ago
pypi.org: cpg-gnomad
Hail utilities for the Genome Aggregation Database
- Homepage: https://github.com/broadinstitute/gnomad_methods
- Documentation: https://broadinstitute.github.io/gnomad_methods/
- License: MIT License
-
Latest release: 0.6.3
published over 3 years ago
Rankings
Forks count: 7.7%
Stargazers count: 8.0%
Dependent packages count: 10.0%
Average: 16.7%
Dependent repos count: 21.7%
Downloads: 35.9%
Maintainers (2)
Last synced:
6 months ago
Dependencies
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actions
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actions
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pypi
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pypi
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requirements.txt
pypi
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pyproject.toml
pypi
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pypi