{"id":21433562,"url":"https://github.com/limix/cellregmap","last_synced_at":"2025-06-11T05:32:49.025Z","repository":{"id":44696428,"uuid":"179108500","full_name":"limix/CellRegMap","owner":"limix","description":"CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq","archived":false,"fork":false,"pushed_at":"2024-08-20T06:26:43.000Z","size":11773,"stargazers_count":22,"open_issues_count":1,"forks_count":3,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-06-05T05:53:34.387Z","etag":null,"topics":["cellregmap","eqtl","limix","sc-eqtl","scrna-seq","structlmm"],"latest_commit_sha":null,"homepage":"","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/limix.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":"2019-04-02T15:35:25.000Z","updated_at":"2025-04-16T18:06:45.000Z","dependencies_parsed_at":"2024-11-22T23:28:50.158Z","dependency_job_id":"7f93bac6-4884-4741-8e4c-411a338277a2","html_url":"https://github.com/limix/CellRegMap","commit_stats":{"total_commits":183,"total_committers":7,"mean_commits":"26.142857142857142","dds":0.5191256830601093,"last_synced_commit":"c9da8e212f6e5ec9734538416193e635ccbcd88b"},"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/limix%2FCellRegMap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/limix%2FCellRegMap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/limix%2FCellRegMap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/limix%2FCellRegMap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/limix","download_url":"https://codeload.github.com/limix/CellRegMap/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/limix%2FCellRegMap/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259207653,"owners_count":22821732,"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":["cellregmap","eqtl","limix","sc-eqtl","scrna-seq","structlmm"],"created_at":"2024-11-22T23:28:47.841Z","updated_at":"2025-06-11T05:32:48.998Z","avatar_url":"https://github.com/limix.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CellRegMap\n\nCellular Regulatory Map (CellRegMap) is a linear mixed model approach to perform multi-context eQTL mapping by leveraging single cell RNA sequencing (scRNA-seq) data.\nIt is related to the previously proposed [StructLMM](https://www.nature.com/articles/s41588-018-0271-0) but importantly it can account for sample structure, including population structure and repeated observations for the same samples, e.g., multiple cells for the same donor.\n\nThe CellRegMap model and its applications to both real and simulated data are described in the [CellRegMap manuscript](https://www.embopress.org/doi/full/10.15252/msb.202110663).\n\nFor more instructions and tutorials to facilitate usage of the package visit [our website](https://limix.github.io/CellRegMap/)!\n\n## Install\n\nFrom your command line, enter\n\n    python3 -m pip install cellregmap\n\nin your command line.\n\n## Development\n\nTo install it in development mode, enter\n\n    git clone https://github.com/limix/CellRegMap.git\n    cd CellRegMap\n    python3 -m pip install -e .\n\nin your command line.\n\n## Installation using a Docker image \nIf you use Docker, you can also pull the [pre-build image from dockerhub](https://hub.docker.com/r/annasecuomo/cellregmap).\n\n\u003c!-- ## Running tests\n\nFrom your command line, enter\n\n    python3 setup.py test --\u003e\n\u003c!-- \n## Project layout\n\n    ├─ old_files/       old scripts\n    ├─ references/      documents on the mathematical concepts\n    └─ CellRegMap/      package implementation\n       └─ test/         test file\n\n## References\n\n- [Exploring Multivariate Gene-Environment Interactions: Models And Applications](https://www.repository.cam.ac.uk/handle/1810/290971)\n- [Optimal tests for rare variant effects in sequencing association studies](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440237/) [Supplementary material](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440237/bin/supp_kxs014_kxs014supp.pdf) --\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flimix%2Fcellregmap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flimix%2Fcellregmap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flimix%2Fcellregmap/lists"}