{"id":31805917,"url":"https://github.com/theislab/atlas-feature-selection-benchmark","last_synced_at":"2025-10-11T03:02:28.656Z","repository":{"id":173300777,"uuid":"525714951","full_name":"theislab/atlas-feature-selection-benchmark","owner":"theislab","description":"Code for \"Feature selection methods affect the performance of scRNA-seq data integration and querying\"","archived":false,"fork":false,"pushed_at":"2024-11-25T17:28:09.000Z","size":68916,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-12-30T12:46:51.676Z","etag":null,"topics":["benchmarking","feature-selection","integration","scrna-seq"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-08-17T09:05:06.000Z","updated_at":"2024-11-25T17:28:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"6ed5749b-80ed-4e41-bfe3-51242892cf8b","html_url":"https://github.com/theislab/atlas-feature-selection-benchmark","commit_stats":null,"previous_names":["theislab/atlas-feature-selection-benchmark"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/atlas-feature-selection-benchmark","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fatlas-feature-selection-benchmark","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fatlas-feature-selection-benchmark/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fatlas-feature-selection-benchmark/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fatlas-feature-selection-benchmark/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/atlas-feature-selection-benchmark/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fatlas-feature-selection-benchmark/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279005972,"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":["benchmarking","feature-selection","integration","scrna-seq"],"created_at":"2025-10-11T03:00:31.173Z","updated_at":"2025-10-11T03:02:28.650Z","avatar_url":"https://github.com/theislab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Atlas feature selection benchmarking\n\n[![PAPER](https://img.shields.io/badge/Nature%20Methods-10.1038%2Fs41592--025--02624--3-eb5b25)](https://doi.org/10.1038/s41592-025-02624-3)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13995812.svg)](https://doi.org/10.5281/zenodo.13995812)\n[![DATA](https://img.shields.io/badge/figshare-10.6084%2Fm9.figshare.c.7521966-a60845?logo=figshare)](https://doi.org/10.6084/m9.figshare.c.7521966)\n\nThis repository contains code for benchmarking the effect of feature selection on scRNA-seq atlas construction and use.\n\nFor more information please refer to the documentation on the [wiki](https://github.com/theislab/atlas-feature-selection-benchmark/wiki).\n\n## Directory structure\n\n* `analysis/` - Notebooks used to perform analysis of the results\n  * `R/` - R functions used in the analysis notebooks\n* `bin/` - Scripts used in **Nextflow** workflows\n  * `functions/` - Functions used across multiple scripts\n* `conf/` - **Nextflow** configuration files\n* `data/` - Data files used in the analysis. Metric score files can downloaded from [figshare](https://figshare.com/articles/dataset/Metric_scores/26390911).\n  * `selected-features/` - Selected features files for each dataset. Can be downloaded from [figshare](https://figshare.com/articles/dataset/Selected_features/26390944).\n* `envs/` - **conda** environment YAML files\n* `output/` - Output from Nextflow workflows (not included in **git**)\n* `reports/` - **RMarkdown** files and functions for output reports generated by the pipeline\n* `work/` - The **Nextflow** working directory (not included in **git**)\n* `workflows/` - **Nextflow** workflow files\n* `LICENSE` - The project license\n* `main.nf` - Main **Nextflow** workflow file\n* `nextflow.config` - Main **Nextflow** config file\n* `README.md` - This README\n* `style_bin.sh` - A script for styling the files in `bin/`\n\n## Data files\n\nData files for this project are available from [figshare](https://doi.org/10.6084/m9.figshare.c.7521966).\nThe analysis reports in the `analysis/` directory assume:\n\n* [Metric files](https://figshare.com/articles/dataset/Metric_scores/26390911) are downloaded to the `data/` directory\n* [Selected features files](https://figshare.com/articles/dataset/Selected_features/26390944) are downloaded to the `data/selected-features/` directory\n\n## Citation\n\nTo refer to this repository, please cite:\n\n\u003e Zappia, L., Ramírez-Suástegui, C., Kfuri-Rubens, R., Vornholz, L., Wang, W., Dietrich, O., Frishberg, A., D Luecken, M. \u0026 J Theis, F. [_Feature selection methods affect the performance of scRNA-seq data integration and querying._](https://doi.org/10.1038/s41592-025-02624-3) Nature methods 1–11 (2025). doi:10.1038/s41592-025-02624-3\n\n```bibtex\n@ARTICLE{Zappia2025,\n  title     = \"{Feature selection methods affect the performance of scRNA-seq\n               data integration and querying}\",\n  author    = \"Zappia, Luke and Richter, Sabrina and Ramírez-Suástegui, Ciro and\n               Kfuri-Rubens, Raphael and Vornholz, Larsen and Wang, Weixu and\n               Dietrich, Oliver and Frishberg, Amit and Luecken, Malte D and\n               Theis, Fabian J\",\n  journal   = \"Nature methods\",\n  publisher = \"Nature Publishing Group\",\n  pages     = \"1--11\",\n  month     =  mar,\n  year      =  2025,\n  doi       = \"10.1038/s41592-025-02624-3\",\n  pmid      =  40082610,\n  issn      = \"1548-7091,1548-7105\",\n  language  = \"en\"\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fatlas-feature-selection-benchmark","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fatlas-feature-selection-benchmark","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fatlas-feature-selection-benchmark/lists"}