https://github.com/broadinstitute/gtex-pipeline
GTEx & TOPMed data production and analysis pipelines
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
1 of 6 committers (16.7%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (4.7%) to scientific vocabulary
Keywords
1ot2od030161
Last synced: 10 months ago
·
JSON representation
Repository
GTEx & TOPMed data production and analysis pipelines
Basic Info
Statistics
- Stars: 367
- Watchers: 25
- Forks: 181
- Open Issues: 16
- Releases: 2
Topics
1ot2od030161
Created over 10 years ago
· Last pushed about 1 year ago
Metadata Files
Readme
License
README.md
Analysis pipelines for the GTEx Consortium and TOPMed
This repository contains analysis pipelines for:
- RNA-seq alignment, quantification, and quality control
- eQTL mapping and annotation
- Allele-specific expression quantification
- Generation of the collapsed annotation used for gene-level expression quantification
Pipeline components are available as docker images, and execution scripts are provided in WDL. The pipelines are available on FireCloud, in the namespace broadinstitute_gtex. All Python scripts are written in Python 3.
A detailed description of the RNA-seq pipeline settings used for TOPMed is provided in TOPMedRNAseqpipeline.md.
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
- Create event: 1
- Release event: 1
- Issues event: 6
- Watch event: 38
- Delete event: 4
- Issue comment event: 4
- Push event: 5
- Pull request event: 3
- Fork event: 9
Last Year
- Create event: 1
- Release event: 1
- Issues event: 6
- Watch event: 38
- Delete event: 4
- Issue comment event: 4
- Push event: 5
- Pull request event: 3
- Fork event: 9
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Francois Aguet | f****s@b****g | 229 |
| Abhishek Choudhary | a****y@g****m | 8 |
| Ted Wong | W****n@g****m | 1 |
| Ross Blanchard | b****s@g****m | 1 |
| Jeremy Leipzig | l****g@g****m | 1 |
| faguet | f****t@i****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 85
- Total pull requests: 24
- Average time to close issues: 5 months
- Average time to close pull requests: 5 days
- Total issue authors: 56
- Total pull request authors: 11
- Average comments per issue: 1.84
- Average comments per pull request: 0.04
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: 5 minutes
- Issue authors: 6
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- xiyasong (5)
- nelsonchanhk (5)
- gouthamatla (4)
- jrxubio (4)
- 52-hertz-whale (3)
- jfertaj (3)
- YantingHuang (3)
- scchess (3)
- KangchengHou (3)
- maegsul (3)
- yingsun-ucsd (3)
- erynes (2)
- methionine23 (2)
- cindywen96 (1)
- raplayer (1)
Pull Request Authors
- abhiachoudhary (19)
- leipzig (3)
- francois-a (2)
- shadizaheri (2)
- jvolkening (1)
- yingsun-ucsd (1)
- yfarjoun (1)
- scchess (1)
- Rosswell (1)
- dampierch (1)
- manwayl (1)
- wormsik (1)