{"id":21480559,"url":"https://github.com/flatironinstitute/inferelator","last_synced_at":"2025-07-12T00:06:20.575Z","repository":{"id":35040943,"uuid":"170143738","full_name":"flatironinstitute/inferelator","owner":"flatironinstitute","description":"Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.","archived":false,"fork":false,"pushed_at":"2024-07-08T16:57:18.000Z","size":25954,"stargazers_count":50,"open_issues_count":6,"forks_count":12,"subscribers_count":9,"default_branch":"release","last_synced_at":"2025-06-18T23:45:41.491Z","etag":null,"topics":["inference","network"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/flatironinstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-02-11T14:35:42.000Z","updated_at":"2025-06-06T09:41:37.000Z","dependencies_parsed_at":"2023-01-15T12:45:40.018Z","dependency_job_id":"a4521bfc-0a18-43bd-9ee4-34c1b575dd7b","html_url":"https://github.com/flatironinstitute/inferelator","commit_stats":{"total_commits":1748,"total_committers":24,"mean_commits":72.83333333333333,"dds":0.562929061784897,"last_synced_commit":"5fd992e9ac22bd11f9df0d8ed352aa7d86e0866c"},"previous_names":[],"tags_count":12,"template":false,"template_full_name":null,"purl":"pkg:github/flatironinstitute/inferelator","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Finferelator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Finferelator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Finferelator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Finferelator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/flatironinstitute","download_url":"https://codeload.github.com/flatironinstitute/inferelator/tar.gz/refs/heads/release","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2Finferelator/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264916028,"owners_count":23682957,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["inference","network"],"created_at":"2024-11-23T12:16:16.319Z","updated_at":"2025-07-12T00:06:19.724Z","avatar_url":"https://github.com/flatironinstitute.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Inferelator 3.0\n\n[![PyPI version](https://badge.fury.io/py/inferelator.svg)](https://badge.fury.io/py/inferelator)\n[![CI](https://github.com/flatironinstitute/inferelator/actions/workflows/python-package.yml/badge.svg)](https://github.com/flatironinstitute/inferelator/actions/workflows/python-package.yml/)\n[![codecov](https://codecov.io/gh/flatironinstitute/inferelator/branch/release/graph/badge.svg)](https://codecov.io/gh/flatironinstitute/inferelator)\n[![Documentation Status](https://readthedocs.org/projects/inferelator/badge/?version=latest)](https://inferelator.readthedocs.io/en/latest/?badge=latest)\n\nThe [Inferelator 3.0](https://doi.org/10.1093/bioinformatics/btac117) is a package for gene regulatory network inference that is based on regularized regression. \nIt is an update of the [Inferelator 2.0](https://ieeexplore.ieee.org/document/5334018), which is an update of the original [Inferelator](https://doi.org/10.1186/gb-2006-7-5-r36)\nIt is maintained by the Bonneau lab in the [Systems Biology group of the Flatiron Institute](https://www.simonsfoundation.org/flatiron/center-for-computational-biology/systems-biology/).\n\nThis repository is the actively developed inferelator package for python. It works for both single-cell and bulk transcriptome experiments.\nIncludes [AMuSR](https://github.com/simonsfoundation/multitask_inferelator/tree/AMuSR/inferelator_ng) \n[(Castro et al 2019)](https://doi.org/10.1371/journal.pcbi.1006591), \nelements of [InfereCLaDR](https://github.com/simonsfoundation/inferelator_ng/tree/InfereCLaDR) \n[(Tchourine et al 2018)](https://doi.org/10.1016/j.celrep.2018.03.048), \nand single-cell workflows [(Jackson et al 2020)](https://elifesciences.org/articles/51254).\n\nWe recommend installing this package from PyPi using `python -m pip install inferelator`. \nIf running locally, also install `joblib` by `python -m pip install joblib` for parallelization.\nIf running on a cluster, also install `dask` by `python -m pip install dask[complete] dask_jobqueue` for dask-based parallelization.\n\nThis package can also be installed from the github repository. \nClone the [inferelator GitHub](https://github.com/flatironinstitute/inferelator) repository and run `python setup.py install`.\n\nDocumentation is available at [https://inferelator.readthedocs.io](https://inferelator.readthedocs.io/en/latest/), and\nbasic workflows for ***Bacillus subtilis*** and ***Saccharomyces cerevisiae*** are included with a tutorial. \n\nAll current example data and scripts are available from Zenodo \n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3355524.svg)](https://doi.org/10.5281/zenodo.3355524).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fflatironinstitute%2Finferelator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fflatironinstitute%2Finferelator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fflatironinstitute%2Finferelator/lists"}