inferelator
Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
Science Score: 54.0%
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
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✓DOI references
Found 11 DOI reference(s) in README -
✓Academic publication links
Links to: ieee.org, zenodo.org -
✓Committers with academic emails
7 of 21 committers (33.3%) from academic institutions -
✓Institutional organization owner
Organization flatironinstitute has institutional domain (flatironinstitute.org) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary
Keywords
Repository
Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
Basic Info
Statistics
- Stars: 50
- Watchers: 9
- Forks: 12
- Open Issues: 6
- Releases: 12
Topics
Metadata Files
README.md
Inferelator 3.0
The Inferelator 3.0 is a package for gene regulatory network inference that is based on regularized regression. It is an update of the Inferelator 2.0, which is an update of the original Inferelator It is maintained by the Bonneau lab in the Systems Biology group of the Flatiron Institute.
This repository is the actively developed inferelator package for python. It works for both single-cell and bulk transcriptome experiments. Includes AMuSR (Castro et al 2019), elements of InfereCLaDR (Tchourine et al 2018), and single-cell workflows (Jackson et al 2020).
We recommend installing this package from PyPi using python -m pip install inferelator.
If running locally, also install joblib by python -m pip install joblib for parallelization.
If running on a cluster, also install dask by python -m pip install dask[complete] dask_jobqueue for dask-based parallelization.
This package can also be installed from the github repository.
Clone the inferelator GitHub repository and run python setup.py install.
Documentation is available at https://inferelator.readthedocs.io, and basic workflows for Bacillus subtilis and Saccharomyces cerevisiae are included with a tutorial.
All current example data and scripts are available from Zenodo
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Owner
- Name: Flatiron Institute
- Login: flatironinstitute
- Kind: organization
- Location: New York City
- Website: https://flatironinstitute.org/
- Repositories: 177
- Profile: https://github.com/flatironinstitute
@SimonsFoundation
GitHub Events
Total
- Watch event: 5
Last Year
- Watch event: 5
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| CJackson | c****r@c****g | 1,346 |
| Nick De Veaux | n****x@g****m | 152 |
| Aaron Watters | a****s@s****g | 98 |
| Claudia Skok Gibbs | c****s@c****g | 59 |
| tymor | t****y@g****m | 31 |
| ryi06 | r****6@h****m | 17 |
| Claudia Skok Gibbs | c****s@c****g | 16 |
| Kostya Tchourine | k****a@n****u | 9 |
| Kostya Tchourine | k****1@n****u | 8 |
| Andreas Tjärnberg | a****5@n****u | 5 |
| Giuseppe Saldi | g****1@2****n | 5 |
| Claudia Skok Gibbs | c****s@f****g | 4 |
| Claudia Skok Gibbs | s****2@g****m | 3 |
| bgorissen | b****n@b****g | 3 |
| Giuseppe SALDI | g****i@g****m | 2 |
| Tymor Hamamsy | t****y@v****g | 2 |
| Nick De Veaux | n****x@N****l | 2 |
| Dayanne Castro | d****o@D****l | 1 |
| Ren Yi | r****8@1****U | 1 |
| Tymor Hamamsy | t****y@w****r | 1 |
| Mahdi Moqri | m****i@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 22
- Total pull requests: 44
- Average time to close issues: 7 months
- Average time to close pull requests: 16 days
- Total issue authors: 18
- Total pull request authors: 7
- Average comments per issue: 2.09
- Average comments per pull request: 0.5
- Merged pull requests: 41
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- frankligy (3)
- poorvam (2)
- torgeihv (2)
- koenvandenberge (1)
- TheChenSu (1)
- sap01 (1)
- spficklin (1)
- rodongo (1)
- IcyFermion (1)
- josruirod (1)
- lichan-upup (1)
- daria-dc (1)
- LouisGil (1)
- zscooper (1)
- raman290307 (1)
Pull Request Authors
- asistradition (34)
- spncrhg (5)
- gs512 (2)
- bgorissen (1)
- Xparx (1)
- moqri (1)
- spficklin (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 139 last-month
- Total dependent packages: 1
- Total dependent repositories: 1
- Total versions: 17
- Total maintainers: 2
pypi.org: inferelator
Inferelator: Network Inference
- Homepage: https://github.com/flatironinstitute/inferelator
- Documentation: https://inferelator.readthedocs.io/
- License: BSD License
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Latest release: 0.6.3
published over 1 year ago
Rankings
Maintainers (2)
Dependencies
- m2r2 *
- sphinx *
- sphinx_rtd_theme *
- dask *
- dask_jobqueue *
- pathos *
- bio-test-artifacts * test
- coverage * test
- pytest * test
- tables * test
- anndata >=0.7.4
- matplotlib >=1.5.1
- numpy >=1.14.0
- pandas >=0.24.0
- scikit-learn *
- scipy >=0.9
- actions/checkout v2 composite
- actions/setup-python v2 composite
- codecov/codecov-action v2 composite