{"id":29303570,"url":"https://github.com/scverse/muon-tutorials","last_synced_at":"2025-10-26T11:37:11.252Z","repository":{"id":69245435,"uuid":"294734436","full_name":"scverse/muon-tutorials","owner":"scverse","description":"Tutorials for multimodal omics data analysis","archived":false,"fork":false,"pushed_at":"2025-02-28T16:20:18.000Z","size":18577,"stargazers_count":13,"open_issues_count":6,"forks_count":7,"subscribers_count":11,"default_branch":"master","last_synced_at":"2025-02-28T21:13:21.248Z","etag":null,"topics":["mudata","multi-omics","muon","scverse","single-cell"],"latest_commit_sha":null,"homepage":"https://muon-tutorials.rtfd.io/","language":"Jupyter Notebook","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/scverse.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":"2020-09-11T15:37:03.000Z","updated_at":"2025-02-28T16:20:21.000Z","dependencies_parsed_at":null,"dependency_job_id":"f6d192bd-f2df-454b-83c1-29c3b2bbe240","html_url":"https://github.com/scverse/muon-tutorials","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/muon-tutorials","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fmuon-tutorials","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fmuon-tutorials/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fmuon-tutorials/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fmuon-tutorials/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/muon-tutorials/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fmuon-tutorials/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263996091,"owners_count":23541402,"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":["mudata","multi-omics","muon","scverse","single-cell"],"created_at":"2025-07-07T01:09:05.949Z","updated_at":"2025-10-08T21:01:52.155Z","avatar_url":"https://github.com/scverse.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Tutorials for multimodal omics data analysis\n\nThis repository contains examples showcasing processing and interpretation of multimodal omics data using [muon](https://github.com/scverse/muon).\n\n## Single-cell ATAC and gene expression\n\n- [These tutorials on 10k PBMC cells](single-cell-rna-atac/pbmc10k) demonstrate how to work with chromatin accessibility and gene expression data from individual cells.\n\n## CITE-seq\n\n- [This tutorial on 5k PBMC cells](cite-seq/1-CITE-seq-PBMC-5k.ipynb) describes how to process CITE-seq data (including antibody-derived tags counts normalisation) and how to integrate surface protein abundance and gene expression.\n\n## Spatiotemporal omics\n\n- [These tutorials](mefisto/) show how smooth factors can be learnt, across time and space, with models such as [MEFISTO](https://biofam.github.io/MOFA2/MEFISTO).\n\n## Biomedical applications\n\n- [Chronic lymphocytic leukemia (CLL) notebook](CLL.ipynb) gives a glimpse of the utility of multi-omics data integration in biomedical applications.\n\n# Other resources\n\nFor the list of software packages, you might find useful the [awesome multi-omics](https://github.com/mikelove/awesome-multi-omics) repository.\n\n[//]: # (numfocus-fiscal-sponsor-attribution)\n\nmuon is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).\nIf you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\n\u003cdiv align=\"center\"\u003e\n\u003ca href=\"https://numfocus.org/project/scverse\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n    width=\"200\"\n  \u003e\n\u003c/a\u003e\n\u003c/div\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fmuon-tutorials","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fmuon-tutorials","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fmuon-tutorials/lists"}