{"id":16320105,"url":"https://github.com/helenalc/catalyst","last_synced_at":"2025-05-16T09:06:47.216Z","repository":{"id":37406036,"uuid":"75288871","full_name":"HelenaLC/CATALYST","owner":"HelenaLC","description":"Cytometry dATa anALYsis Tools","archived":false,"fork":false,"pushed_at":"2025-05-09T09:42:47.000Z","size":136176,"stargazers_count":68,"open_issues_count":16,"forks_count":31,"subscribers_count":11,"default_branch":"main","last_synced_at":"2025-05-09T10:40:45.400Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","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/HelenaLC.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","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,"publiccode":null,"codemeta":null}},"created_at":"2016-12-01T12:06:28.000Z","updated_at":"2025-05-09T09:42:15.000Z","dependencies_parsed_at":"2023-02-16T22:01:00.696Z","dependency_job_id":"7cc8bc7a-4cbc-4be5-bd30-1fa56776988a","html_url":"https://github.com/HelenaLC/CATALYST","commit_stats":{"total_commits":2865,"total_committers":37,"mean_commits":77.43243243243244,"dds":0.3776614310645724,"last_synced_commit":"f3e294ed9a4d3f300feb994bb381df6a6b2c8309"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FCATALYST","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FCATALYST/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FCATALYST/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HelenaLC%2FCATALYST/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HelenaLC","download_url":"https://codeload.github.com/HelenaLC/CATALYST/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254501558,"owners_count":22081528,"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":[],"created_at":"2024-10-10T22:29:05.611Z","updated_at":"2025-05-16T09:06:42.203Z","avatar_url":"https://github.com/HelenaLC.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Welcome to `CATALYST` \u003cimg src=\"inst/extdata/sticker.png\" width=\"200\" align=\"right\" /\u003e\n\n`CATALYST` leverages existing R/Bioconductor infrastructure by building around Biocondcutor's `SingleCellExperiment` class, and by providing an interface for conversion to other data structures established in the cytometry community (e.g., `flowCore`'s `flowFrame/Set` classes), thus facilitating communication with existing tools for visualization (e.g., `ggcyto`) and gating (e.g., `openCyto`).  The package currently provides:\n\n- an extensive suit of visualizations for differential discovery\n- a pipeline for preprocessing of cytometry data, including\n  - normalization using bead standards\n  - single-cell deconvolution\n  - bead-based compensation\n  \n### References\n\n- Chevrier S\u003csup\u003e\u0026#9734;\u003c/sup\u003e, Crowell HL\u003csup\u003e\u0026#9734;\u003c/sup\u003e, Zanotelli VRT\u003csup\u003e\u0026#9734;\u003c/sup\u003e, Engler S, Robinson MD \u0026 Bodenmiller B (2018):  \n*Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry*. Cell Systems 6(5):612-620.e5. \n- Nowicka M, Krieg C, Crowell HL, Weber LM, Hartmann FJ, Guglietta S, Becher B, Levesque MP \u0026 Robinson MD (2017):  \n*CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets*. F1000Resaearch 6:748. \n\n---\n\n### Got a problem (or an idea)?\n\n`CATALYST` is still under active development. We greatly welcome (and highly encourage!) all feedback, bug reports and suggestions for improvement [HERE](https://github.com/HelenaLC/CATALYST/issues). **Please make sure to raise issues with a reproducible example and the output of your `sessionInfo()`.**","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fcatalyst","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhelenalc%2Fcatalyst","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhelenalc%2Fcatalyst/lists"}