{"id":28461821,"url":"https://github.com/pinellolab/pychromvar","last_synced_at":"2025-07-03T14:32:49.774Z","repository":{"id":65507460,"uuid":"493414054","full_name":"pinellolab/pychromVAR","owner":"pinellolab","description":"A python package for chromVAR","archived":false,"fork":false,"pushed_at":"2023-05-01T23:20:59.000Z","size":2696,"stargazers_count":28,"open_issues_count":3,"forks_count":4,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-06-07T04:07:38.272Z","etag":null,"topics":["chromatin-accessibiity","chromvar","scatac-seq"],"latest_commit_sha":null,"homepage":"https://pychromvar.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pinellolab.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}},"created_at":"2022-05-17T21:07:15.000Z","updated_at":"2025-05-08T14:23:43.000Z","dependencies_parsed_at":"2023-07-26T13:07:21.802Z","dependency_job_id":null,"html_url":"https://github.com/pinellolab/pychromVAR","commit_stats":null,"previous_names":["lzj1769/pychromvar"],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/pinellolab/pychromVAR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pinellolab%2FpychromVAR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pinellolab%2FpychromVAR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pinellolab%2FpychromVAR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pinellolab%2FpychromVAR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pinellolab","download_url":"https://codeload.github.com/pinellolab/pychromVAR/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pinellolab%2FpychromVAR/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263342291,"owners_count":23451982,"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":["chromatin-accessibiity","chromvar","scatac-seq"],"created_at":"2025-06-07T04:07:38.314Z","updated_at":"2025-07-03T14:32:49.767Z","avatar_url":"https://github.com/pinellolab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Stars](https://img.shields.io/github/stars/lzj1769/pychromVAR?logo=GitHub\u0026color=yellow)](https://github.com/lzj1769/pychromVAR/stargazers)\n[![PyPI](https://img.shields.io/pypi/v/pychromvar?logo=PyPI)](https://pypi.org/project/pychromvar/)\n[![Docs](https://readthedocs.org/projects/pychromvar/badge/?version=latest)](https://pychromvar.readthedocs.io)\n\n# pychromVAR \n\npychromVAR is a python package for inferring transcription factor binding variability from scATAC-seq data by implmenting the algorithm proposed in [chromVAR](https://github.com/GreenleafLab/chromVAR). It is built on [anndata](https://anndata.readthedocs.io/en/latest/) and [mudata](https://mudata.readthedocs.io/en/latest/) therefore can work seamlessly with [Scanpy](https://scanpy.readthedocs.io/en/stable/index.html) and [Muon](https://gtca.github.io/muon/) pipeline. \n\nFor more methodological details, please refer to the [paper](https://www.nature.com/articles/nmeth.4401). \n\n# Installation\n\nThe quickest and easiest way to get pychromvar is to to use pip:\n\n```shell\npip install pychromvar\n```\n\n# Ecosystem\n\npychromVAR is part of [scverse](https://scverse.org/packages/#ecosystem) ecosystem.\n\n# Tutorial\n\nYou can find [here](https://pychromvar.readthedocs.io/en/latest/notebooks/multimodal_pbmc_3k.html) a tutorial how to use pychromVAR combined with Muon to analysis multimodal single-cell PBMC data.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpinellolab%2Fpychromvar","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpinellolab%2Fpychromvar","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpinellolab%2Fpychromvar/lists"}