{"id":29701216,"url":"https://github.com/ilia-kats/mudata","last_synced_at":"2025-08-24T14:13:47.562Z","repository":{"id":69245319,"uuid":"405976866","full_name":"ilia-kats/MuData","owner":"ilia-kats","description":"MuData-compatible storage for bioconductor's MultiAssayExperiment","archived":false,"fork":false,"pushed_at":"2025-02-24T16:48:16.000Z","size":9000,"stargazers_count":6,"open_issues_count":2,"forks_count":4,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-07-13T23:21:45.831Z","etag":null,"topics":["anndata","bioconductor","mudata","multi-omics","multimodal-omics","scrna-seq"],"latest_commit_sha":null,"homepage":"https://ilia-kats.github.io/MuData/","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/ilia-kats.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-09-13T13:05:34.000Z","updated_at":"2025-06-22T19:34:27.000Z","dependencies_parsed_at":"2025-02-24T16:56:01.687Z","dependency_job_id":null,"html_url":"https://github.com/ilia-kats/MuData","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ilia-kats/MuData","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ilia-kats%2FMuData","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ilia-kats%2FMuData/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ilia-kats%2FMuData/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ilia-kats%2FMuData/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ilia-kats","download_url":"https://codeload.github.com/ilia-kats/MuData/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ilia-kats%2FMuData/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266665813,"owners_count":23964974,"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":"2025-07-23T02:00:09.312Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"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":["anndata","bioconductor","mudata","multi-omics","multimodal-omics","scrna-seq"],"created_at":"2025-07-23T11:08:31.357Z","updated_at":"2025-07-23T11:08:32.165Z","avatar_url":"https://github.com/ilia-kats.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MuData\n\n[![R-CMD-check](https://github.com/ilia-kats/MuData/workflows/R-CMD-check/badge.svg)](https://github.com/ilia-kats/MuData/actions) [![pkgdown](https://github.com/ilia-kats/MuData/workflows/pkgdown/badge.svg)](https://github.com/ilia-kats/MuData/actions)\n\n[Documentation](https://ilia-kats.github.io/MuData/) | [Preprint](https://www.biorxiv.org/content/10.1101/2021.06.01.445670v1) | [Discord](https://discord.com/invite/MMsgDhnSwQ)\n\n`MuData` is a package that provides I/O functionality for `.h5mu` files and [MultiAssayExperiment](http://waldronlab.io/MultiAssayExperiment/) objects.\n\nYou can learn more about multimodal data containers in the reference [`mudata` documentation](https://mudata.readthedocs.io/en/latest/io/mudata.html).\n\n## Installation\n\n`MuData` uses [`rhdf5`](https://bioconductor.org/packages/devel/bioc/html/rhdf5.html) to access `.h5mu` and `.h5ad` files. In the meantime, the bioc-devel version of `rhdf5` must be used. \n\n`rhdf5` and `MuData` can be installed by running\n\n```R\nremotes::install_github(\"grimbough/rhdf5\")\nremotes::install_github(\"ilia-kats/MuData\")\n```\n\nWe use `rhdf5` over `hdf5r` to stay compatible with the rest of the Bioconductor ecosystem.\nIn particular, using `hdf5r` would make integrating with other packages building on `rhdf5`, such as `HDF5Array`, much more difficult, if not impossible. We have implemented necessary HDF5 features that the `.h5ad` and consequently `.h5mu` formats make use of upstream, including [file creation properties](https://github.com/grimbough/rhdf5/pull/95) and [object references](https://github.com/grimbough/rhdf5/pull/96).\n\n\n## Quick start\n\n`MuData` provides a set of I/O operations for multimodal data.\n\n`MuData` implements `WriteH5MU()` that saves MultiAssayExperiment objects to `.h5mu` files that can be further integrated into workflows in multiple programming languages, including the [`muon` Python library](https://github.com/scverse/muon) and the [`Muon.jl` Julia library](https://github.com/scverse/Muon.jl). `ReadH5MU()` reads `.h5mu` files into MultiAssayExperiment objects.\n\n\n### Writing files\n\nStart with an existing dataset, e.g. a [MultiAssayExperiment](http://waldronlab.io/MultiAssayExperiment/) object with five distinct modalities:\n\n```R\nlibrary(MultiAssayExperiment)\ndata(miniACC)\n```\n\n`WriteH5MU()` allows to save the object into a `.h5mu` file:\n\n```R\nlibrary(MuData)\nWriteH5MU(miniACC, \"miniACC.h5mu\")\n```\n\n### Reading files\n\n```R\nminiACC \u003c- ReadH5MU(\"miniACC.h5mu\")\n```\n\n## Relevant projects\n\nOther R packages for multimodal I/O include:\n\n- [MuDataSeurat](https://github.com/PMBio/MuDataSeurat) for [Seurat](https://github.com/satijalab/seurat/) objects\n- [SeuratDisk](https://github.com/mojaveazure/seurat-disk)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Filia-kats%2Fmudata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Filia-kats%2Fmudata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Filia-kats%2Fmudata/lists"}