{"id":31805798,"url":"https://github.com/theislab/multicpa","last_synced_at":"2025-10-11T02:58:42.421Z","repository":{"id":44456045,"uuid":"510699390","full_name":"theislab/multicpa","owner":"theislab","description":null,"archived":false,"fork":false,"pushed_at":"2022-07-08T10:12:17.000Z","size":278,"stargazers_count":13,"open_issues_count":1,"forks_count":2,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-18T15:24:07.252Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/theislab.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}},"created_at":"2022-07-05T11:04:15.000Z","updated_at":"2024-05-05T13:21:16.000Z","dependencies_parsed_at":"2022-09-01T02:02:20.498Z","dependency_job_id":null,"html_url":"https://github.com/theislab/multicpa","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/multicpa","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmulticpa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmulticpa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmulticpa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmulticpa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/multicpa/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmulticpa/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279005950,"owners_count":26084009,"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","status":"online","status_checked_at":"2025-10-11T02:00:06.511Z","response_time":55,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2025-10-11T02:58:40.022Z","updated_at":"2025-10-11T02:58:42.413Z","avatar_url":"https://github.com/theislab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MultiCPA\n\n`MultiCPA` is a research project from a computatiobal biology group of Prof. Fabian \nTheis (https://github.com/theislab) from Helmholtz Zentrum München. \n\n## What is MultiCPA?\n![Screenshot](Figure.png)\n\n`MultiCPA` is a framework to learn effects of perturbations at the single-cell level for multiple modalities: `proteins` and `mRNAs`. \nMultiCPA encodes and learns phenotypic drug response across different cell types, doses and drug combinations. MultiCPA allows:\n\n* Out-of-distribution predicitons of unseen drug combinations at various doses and among different cell types.\n* Learn interpretable drug and cell type latent spaces.\n* Estimate dose response curve for each perturbation and their combinations.\n* Access the uncertainty of the estimations of the model.\n\n## Package Structure\n\nThe repository is centered around the `MultiCPA` module:\n\n* [`MultiCPA.train`](MultiCPA/train.py) contains scripts to train the model.\n* [`MultiCPA.api`](MultiCPA/api.py) contains user friendly scripts to interact with the model via scanpy.\n* [`MultiCPA.plotting`](MultiCPA/plotting.py) contains scripts to plotting functions.\n* [`MultiCPA.model`](MultiCPA/model.py) contains modules of compert model.\n* [`MultiCPA.data`](MultiCPA/data.py) contains data loader, which transforms anndata structure to a class compatible with compert model.\n\nAdditional files and folders for reproducibility are found in another repository: [multicpa-reproducibility](https://github.com/theislab/multicpa-reproducibility)\n\n* [`datasets`](datasets/) contains both versions of the data: raw and pre-processed.\n* [`preprocessing`](preprocessing/) contains notebooks to reproduce the datasets pre-processing from raw data.\n* [`notebooks`](notebooks/) contains notebooks to reproduce plots from the paper and detailed analysis of each of the datasets.\n* [`figures`](figures/) contains figures after running the notebooks.\n\nNote that the codebase was build on top of `CPA` model.\n\n## Usage\n\nTo learn how to use this repository, check [example_training.ipynb](https://github.com/theislab/multicpa-reproducibility/blob/main/notebooks/example_training.ipynb).\nNote that hyperparameters in the demo are not default and will not work for new datasets. Please make\nsure to run `seml` sweeps for your new dataset to find best hyperparameters. Provided Conda environments are strongly recommended. \n\n## Examples and Reproducibility\nAll the examples and the reproducibility notebooks for the plots in the paper could be found in the [multicpa-reproducibility](https://github.com/theislab/multicpa-reproducibility) repository.\n\n## Documentation\n\nCurrently, you can access the documentation via `help` function in IPython. For example:\n\n```python\nfrom MultiCPA.api import ComPertAPI\n\nhelp(ComPertAPI)\n\nfrom MultiCPA.plotting import CompertVisuals\n\nhelp(CompertVisuals)\n\n```\n\nA separate page with the documentation is coming soon.\n\n## Support and contribute\n\nIf you have a question or noticed a problem, you can post an [`issue`](https://github.com/theislab/multicpa/).\n\n## License\n\nThis source code is released under the BSD 3-Clause License, included [here](LICENSE).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fmulticpa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fmulticpa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fmulticpa/lists"}