https://github.com/broadinstitute/abc-enhancer-gene-prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
https://github.com/broadinstitute/abc-enhancer-gene-prediction
Science Score: 57.0%
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Found 2 DOI reference(s) in README -
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Links to: nature.com -
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Organization broadinstitute has institutional domain (www.broadinstitute.org) -
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○Scientific vocabulary similarity
Low similarity (8.1%) to scientific vocabulary
Repository
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
Basic Info
Statistics
- Stars: 236
- Watchers: 13
- Forks: 69
- Open Issues: 6
- Releases: 10
Metadata Files
README.md
CircleCI 
:memo: Note: This repository is the version of ABC presented in Gschwind et al. (BioRxiv 2023) and is a revamp of the original ABC codebase. To access any previous version of ABC, please visit https://github.com/EngreitzLab/ABC-Enhancer-Gene-Prediction-20250314-archive. - For the version of ABC presented in Fulco et al. (Nat. Genet. 2019)[1], use the NG2019 branch of the archived repo - For the version of ABC presented in Nasser et al. (Nature 2021), use the master branch of the archived repo
We have documented the codebase and usage in Read The Docs
Activity by Contact Model of Enhancer-Gene Specificity
The Activity-by-Contact (ABC) model predicts which enhancers regulate which genes on a cell type specific basis. This repository contains the code needed to run the ABC model as well as small sample data files, example commands, and some general tips and suggestions.
If you use the ABC model in published research, please cite:
[1] Fulco CP, Nasser J, Jones TR, Munson G, Bergman DT, Subramanian V, Grossman SR, Anyoha R, Doughty BR, Patwardhan TA, Nguyen TH, Kane M, Perez EM, Durand NC, Lareau CA, Stamenova EK, Aiden EL, Lander ES & Engreitz JM. Activity-by-contact model of enhancerpromoter regulation from thousands of CRISPR perturbations. Nat. Genet. 51, 16641669 (2019). https://www.nature.com/articles/s41588-019-0538-0
Contact
Please submit a GitHub issue with any questions or if you experience any issues/bugs.
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: 12
- Issues event: 23
- Watch event: 26
- Delete event: 36
- Member event: 1
- Issue comment event: 38
- Push event: 61
- Pull request review comment event: 2
- Pull request review event: 6
- Pull request event: 21
- Fork event: 8
Last Year
- Create event: 12
- Issues event: 23
- Watch event: 26
- Delete event: 36
- Member event: 1
- Issue comment event: 38
- Push event: 61
- Pull request review comment event: 2
- Pull request review event: 6
- Pull request event: 21
- Fork event: 8
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 16
- Total pull requests: 9
- Average time to close issues: about 2 years
- Average time to close pull requests: 3 days
- Total issue authors: 15
- Total pull request authors: 2
- Average comments per issue: 2.25
- Average comments per pull request: 0.0
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 9
- Average time to close issues: 3 months
- Average time to close pull requests: 3 days
- Issue authors: 4
- Pull request authors: 2
- Average comments per issue: 2.6
- Average comments per pull request: 0.0
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
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Pull Request Authors
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Dependencies
- sphinx_rtd_theme *