{"id":31805817,"url":"https://github.com/theislab/spapros_reproducibility","last_synced_at":"2026-06-12T16:31:32.867Z","repository":{"id":78601091,"uuid":"440153283","full_name":"theislab/spapros_reproducibility","owner":"theislab","description":null,"archived":false,"fork":false,"pushed_at":"2024-03-29T20:44:38.000Z","size":12664,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-01-15T00:52:42.838Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"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":null,"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}},"created_at":"2021-12-20T11:55:44.000Z","updated_at":"2025-06-27T12:24:57.000Z","dependencies_parsed_at":"2023-04-06T03:02:16.536Z","dependency_job_id":null,"html_url":"https://github.com/theislab/spapros_reproducibility","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/spapros_reproducibility","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros_reproducibility","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros_reproducibility/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros_reproducibility/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros_reproducibility/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/spapros_reproducibility/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fspapros_reproducibility/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34253928,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-12T02:00:06.859Z","response_time":109,"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":"2025-10-11T02:58:57.224Z","updated_at":"2026-06-12T16:31:32.862Z","avatar_url":"https://github.com/theislab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# spapros_reproducibility\n\nThis repository contains the code to reproduce the analyses and figures of the manuscript \"Probeset selection for targeted spatial transcriptomics\". The manuscript is currently under review. Preprint at [bioRxiv](https://doi.org/10.1101/2022.08.16.504115).\n\nThe repository is structured as follows:\n- preprint folder: contains the scripts and notebooks to reproduce the analyses and figures till the preprint version. This includes Figures 1c, 2c,d,e 3, S1, S2a, S3, S4, S5, S6, S7, S9b,c.\n- revision folder: contains the scripts and notebooks to reproduce the analyses and figures for the revised version of the manuscript. This includes Figures 4, S2b, S8, S9a, S10, S11, S12, S13.\n- For the revised version we ran extensive benchmarks with our snakemake pipeline (release tag 0.1.0). The configurations for rerunning the experiments can be found [there](https://github.com/theislab/spapros-smk) at `spapros-smk/configs/` with the file names `config_rev.yaml`, `config_rev_bm.yaml`, `config_rev_bm_probes.yaml`.\n\nPlease do not hesitate to open an issue in case of any questions or issues.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fspapros_reproducibility","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fspapros_reproducibility","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fspapros_reproducibility/lists"}