{"id":20751304,"url":"https://github.com/cbg-ethz/scdna-pipe","last_synced_at":"2026-01-05T11:35:14.141Z","repository":{"id":242873220,"uuid":"221738204","full_name":"cbg-ethz/scdna-pipe","owner":"cbg-ethz","description":"Python data analysis pipeline for single cell copy number event history reconstruction","archived":false,"fork":false,"pushed_at":"2024-05-29T12:57:27.000Z","size":17638,"stargazers_count":2,"open_issues_count":3,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-01-28T02:42:46.476Z","etag":null,"topics":["bioinformatics","bioinformatics-pipeline","data-analysis","genomics","python","snakemake","snakemake-workflows","workflow"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cbg-ethz.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":"2019-11-14T16:14:41.000Z","updated_at":"2024-06-05T10:55:55.000Z","dependencies_parsed_at":"2024-06-05T13:33:46.092Z","dependency_job_id":"d76d1218-e167-4560-8a9f-91c8fc17e4df","html_url":"https://github.com/cbg-ethz/scdna-pipe","commit_stats":null,"previous_names":["cbg-ethz/scdna-pipe"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2Fscdna-pipe","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2Fscdna-pipe/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2Fscdna-pipe/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbg-ethz%2Fscdna-pipe/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbg-ethz","download_url":"https://codeload.github.com/cbg-ethz/scdna-pipe/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245031516,"owners_count":20549926,"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":["bioinformatics","bioinformatics-pipeline","data-analysis","genomics","python","snakemake","snakemake-workflows","workflow"],"created_at":"2024-11-17T08:32:34.293Z","updated_at":"2026-01-05T11:35:14.047Z","avatar_url":"https://github.com/cbg-ethz.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Single-cell DNA Analysis \u003cimg src=\"figures/logo.png\" align=\"right\" width=\"160\"\u003e\n\n[![CircleCI](https://circleci.com/gh/cbg-ethz/scdna-pipe.svg?style=svg\u0026circle-token=60921152e3353ae7cd6d5e13d14158bcbde57973)](https://circleci.com/gh/cbg-ethz/scdna-pipe)\n[![License](http://img.shields.io/:license-Apache%202-green.svg)](http://www.apache.org/licenses/LICENSE-2.0.txt)\n[![Python Version](https://img.shields.io/badge/python-3-blue.svg)](https://img.shields.io/badge/python-3-blue.svg)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n\n## About\nReproducible Python pipeline for genomic data analysis. Performs single-cell copy number variation calling by learning the underlying tumour evolution history by state-of-the-art phylogenetic tree reconstruction method: SCICoNE. The pipeline is built using Python, Conda environment management system and the Snakemake workflow management system. The pipeline starts from the raw sequencing files and a settings file for the parameter configurations. After the analysis, it produces a report and multiple figures to inform the treatment decision of the cancer patient.\n\nThe pipeline makes use of `scgenpy`, a package that exposes functions for preprocessing, postprocessing and plotting data, allowing you to interact with data outside the pipeline context.\n\n## Installing\n1. Clone the repository\n2. Install and update using `pip`:\n  ```bash\n  pip install -e .\n  ```\n3. Install SCICoNE.\n\n## Running\n1. Prepare the configuration file according to your analysis\n2. Run `snakemake` with:\n  ```bash\n  snakemake --configfile your_config_file\n  ```\n3. (Optional) Refer to https://snakemake.readthedocs.io to customise your `snakemake` for your environment\n\n## Contributing\n\nYou are very welcome to contribute! You can start with the existing issues or create new issues.\nMake sure to follow the CI checks. Use the [pre-commit hook](https://github.com/cbg-ethz/scdna-pipe/blob/master/.pre-commit-config.yaml) defined in the project to meet the code style. If you are adding new functionality, add the corresponding test as well in order to keep the code coverage high.\n\n## License\n\nThis project is licensed under the Apache License - see the [LICENSE](LICENSE) file for details\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fscdna-pipe","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcbg-ethz%2Fscdna-pipe","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbg-ethz%2Fscdna-pipe/lists"}