omicsintegrator
Prize-Collecting Steiner Forests for Interactomes
Science Score: 10.0%
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
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
5 of 8 committers (62.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.1%) to scientific vocabulary
Keywords
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Repository
Prize-Collecting Steiner Forests for Interactomes
Basic Info
- Host: GitHub
- Owner: fraenkel-lab
- License: bsd-3-clause
- Language: Jupyter Notebook
- Default Branch: master
- Homepage: https://fraenkel-lab.github.io/OmicsIntegrator2
- Size: 39.8 MB
Statistics
- Stars: 60
- Watchers: 9
- Forks: 21
- Open Issues: 16
- Releases: 1
Topics
Metadata Files
README.md
OmicsIntegrator2
Background
Omics Integrator is a package designed to integrate proteomic data, gene expression data and/or epigenetic data using a protein-protein interaction network. It identifies high-confidence, relevant subnetworks from the underlying interactome. It is comprised of two modules, Garnet and Forest. This repository holds the code for Forest in version 2 of Omics Integrator.
Forest first maps your high-throughput data onto the network. Proteins in the network are 'nodes' connected by edges representing physical interactions of two protein nodes. You should assign protein nodes prizes from your high-throughput data, i.e. the prize could be the log fold change of that protein in your system. The edges are assigned costs, often proportional to the confidence in that interaction.
Forest then adds a 'dummy node' to the network with edges to all of the nodes you've assigned prizes, called terminals. There are several parameters you can change in Forest. Omega, the cost of the edges between the root dummy node and the terminals, determines the number of pathways in the final solution. Beta, the relative weighting between node prizes and edge costs, determines the size of the final solution. And alpha adds a penalty to edges based on the degrees of the two nodes that the edge connects. This keeps the network from being biased towards "hub nodes", often highly studied and promiscuous proteins that may not be specific to your system.
Finally, Forest uses the Prize-Collecting Steiner Forest algorithm to whittle the large interactome down to relevant sub-networks, or pathways. These pathways are likely places to look for important cellular functions altered in your system. They will include some, but not all, of your terminals. They may also include "Steiner nodes", nodes that you did not assign a prize to, but that the algorithm is predicting are important to the pathways altered in your system.
With the output of these sub-networks, Omics Integrator allows researchers to go from huge, often contradictory lists of genes, proteins, and metabolites from multiple -omics data sources to a few important cellular pathways to focus on in follow-up studies of their system.
Changelog:
6/20/18: 2.3.0
- Many breaking changes, e.g. method names, data formats
- Add tests
- New annotation file contains process and function gene annotations on top of subcellular localizations.
- HTML visualization improvements
- First release with a changelog entry and github release!
Owner
- Name: The Fraenkel Lab at MIT
- Login: fraenkel-lab
- Kind: organization
- Email: apply.fraenkel@mit.edu
- Location: Cambridge, MA
- Website: http://fraenkel.mit.edu/
- Repositories: 15
- Profile: https://github.com/fraenkel-lab
We are developing computational and experimental approaches to search for new therapeutic strategies for diseases.
GitHub Events
Total
- Watch event: 4
- Fork event: 1
Last Year
- Watch event: 4
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Alexander Lenail | z****e@g****m | 98 |
| Alexander Lenail | a****x@l****g | 31 |
| Amanda Kedaigle | m****y@m****u | 18 |
| Jonathan Li | j****i@m****u | 14 |
| Johnny Li | i****i@m****u | 11 |
| divyaramamoorthy | d****y@g****m | 4 |
| Alexander Lenail | a****l@t****u | 2 |
| Clemens Hug | c****g@h****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 56
- Total pull requests: 47
- Average time to close issues: 5 months
- Average time to close pull requests: 8 days
- Total issue authors: 11
- Total pull request authors: 6
- Average comments per issue: 2.68
- Average comments per pull request: 1.32
- Merged pull requests: 40
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- alexlenail (26)
- iamjli (15)
- agitter (4)
- AmandaKedaigle (3)
- brycehwang (2)
- natashapm (1)
- matthewfallan (1)
- bblum9 (1)
- sgosline (1)
- robd02130 (1)
- divyaramamoorthy (1)
Pull Request Authors
- alexlenail (29)
- iamjli (14)
- AmandaKedaigle (3)
- dependabot[bot] (2)
- clemenshug (1)
- agitter (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 12 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 4
- Total maintainers: 1
pypi.org: omicsintegrator
- Homepage: https://github.com/fraenkel-lab/OmicsIntegrator2
- Documentation: https://omicsintegrator.readthedocs.io/
- License: MIT
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Latest release: 2.3.10
published about 7 years ago
Rankings
Maintainers (1)
Dependencies
- axial >=0.0.4
- goenrich ==1.7.0
- jinja2 >=2.9
- networkx >=2.1
- numpy >=1.12.0
- pandas >=0.21.1
- pcst_fast >=1.0.6
- python-louvain >=0.9
- scikit-learn >=0.19.0
- scipy >=1.1.0
- axial *
- goenrich *
- networkx ==2.1
- numpy *
- pandas ==0.23.4
- pcst_fast ==1.0.7
- python-louvain *
- scipy *
- sklearn *