{ "_id": "6adfe9b093f02b9aed97960f", "Package": "MuData", "Title": "Serialization for MultiAssayExperiment Objects", "Version": "1.17.1", "Authors@R": "c(person(given = \"Danila\",\nfamily = \"Bredikhin\",\nrole = c(\"aut\"),\nemail = \"danila.bredikhin@embl.de\",\ncomment = c(ORCID = \"0000-0001-8089-6983\")),\nperson(given = \"Ilia\",\nfamily = \"Kats\",\nrole = c(\"aut\", \"cre\"),\nemail = \"i.kats@dkfz-heidelberg.de\",\ncomment = c(ORCID = \"0000-0001-5220-5671\")))", "Description": "Save MultiAssayExperiments to h5mu files supported by muon\nand mudata. Muon is a Python framework for multimodal omics\ndata analysis. It uses an HDF5-based format for data storage.", "URL": "https://github.com/ilia-kats/MuData", "BugReports": "https://github.com/ilia-kats/MuData/issues", "VignetteBuilder": "knitr", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "Config/testthat/edition": "3", "biocViews": "DataImport", "Config/pak/sysreqs": "libicu-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-26 16:56:11 UTC", "RemoteUrl": "https://github.com/bioc/MuData", "RemoteRef": "HEAD", "RemoteSha": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-26 23:32:11 UTC", "User": "root" }, "Author": "Danila Bredikhin [aut] (ORCID: ),\nIlia Kats [aut, cre] (ORCID: )", "Maintainer": "Ilia Kats ", "_user": "bioc", "_type": "src", "_file": "MuData_1.17.1.tar.gz", "_fileid": "https://r2.ropensci.org/f31a116da1a1c096a43ddbf35a77dd844e16c1f9939bbb0f8c035d0b861ca665", "_filesize": 1257870, "_sha256": "f31a116da1a1c096a43ddbf35a77dd844e16c1f9939bbb0f8c035d0b861ca665", "_expires": "2027-02-04T00:00:46.000Z", "_created": "2026-10-26T23:32:11.000Z", "_published": "2026-10-27T00:00:48.344Z", "_upstream": "https://github.com/bioc/MuData", "_status": "success", "_maintainer": { "name": "Ilia Kats", "email": "i.kats@dkfz-heidelberg.de", "login": "ilia-kats", "orcid": "0000-0001-5220-5671", "description": "", "uuid": 3499574 }, "_jobs": [ { "job": 121913459109, "time": 350, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "12696433815" }, { "job": 121913459175, "time": 334, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12697598795" }, { "job": 121913459107, "time": 486, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12698035022" }, { "job": 121913459198, "time": 215, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12698137452" }, { "job": 121913459156, "time": 292, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12699381227" }, { "job": 121909339598, "time": 642, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12696278190" }, { "job": 121913459046, "time": 311, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12696598764" }, { "job": 121913459164, "time": 426, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12696189494" }, { "job": 121913459099, "time": 532, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12697069000" }, { "job": 121913459356, "time": 521, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12696589030" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40419237663", "_commit": { "id": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "author": "Ilia Kats ", "committer": "Ilia Kats ", "message": "Merge branch 'master' into devel\n", "time": 1793033771 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "Matrix", "role": "Depends" }, { "package": "S4Vectors", "role": "Depends" }, { "package": "rhdf5", "version": ">= 2.45", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "MultiAssayExperiment", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "DelayedArray", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "HDF5Array", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "fs", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "SingleCellMultiModal", "role": "Suggests" }, { "package": "CiteFuse", "role": "Suggests" }, { "package": "scater", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-44", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "dataimport", "anndata", "bioconductor", "mudata", "multi-omics", "multimodal-omics", "scrna-seq" ], "_stars": 11, "_contributors": [ { "user": "ilia-kats", "count": 77, "uuid": 3499574 }, { "user": "gtca", "count": 63, "uuid": 32863903 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 2, "uuid": 2746443 }, { "user": "wolski", "count": 2, "uuid": 1926513 }, { "user": "votti", "count": 1, "uuid": 3743016 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 464, "source": "https://www.bioconductor.org/packages/stats/bioc/MuData" }, "_devurl": "https://github.com/ilia-kats/mudata", "_searchresults": 50, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/MuData.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/ilia-kats/mudata", "_realowner": "bioc", "_cranurl": false, "_exports": [ "readH5AD", "readH5MU", "writeH5AD", "writeH5MU" ], "_help": [ { "page": "readH5AD", "title": "Read an .h5ad file and create a 'SingleCellExperiment'.", "topics": [ "readH5AD" ] }, { "page": "readH5MU", "title": "Read an .h5mu file and create a 'MultiAssayExperiment'.", "topics": [ "readH5MU" ] }, { "page": "writeH5AD", "title": "Save an experiment to an .h5ad file.", "topics": [ "writeH5AD" ] }, { "page": "writeH5MU", "title": "Save a 'MultiAssayExperiment' to an .h5mu file.", "topics": [ "writeH5MU" ] } ], "_readme": "https://github.com/bioc/MuData/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocBaseUtils", "BiocGenerics", "biocmake", "cli", "cpp11", "DelayedArray", "dir.expiry", "dplyr", "filelock", "generics", "GenomicRanges", "glue", "IRanges", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "MultiAssayExperiment", "pillar", "pkgconfig", "purrr", "R6", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XVector" ], "_vignettes": [ { "source": "Blood-CITE-seq.Rmd", "filename": "Blood-CITE-seq.html", "title": "CITE-seq data with CiteFuse and MuData", "author": "Danila Bredikhin, Ilia Kats", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Loading libraries", "Loading data", "Processing count matrices", "Making a MultiAssayExperiment object", "Writing to H5MU", "References", "Session Info" ], "created": "2021-12-10 03:03:44", "modified": "2022-01-10 14:31:59", "commits": 5 }, { "source": "Cord-Blood-CITE-seq.Rmd", "filename": "Cord-Blood-CITE-seq.html", "title": "CITE-seq data with MultiAssayExperiment and MuData", "author": "Danila Bredikhin, Ilia Kats", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Loading libraries", "Loading data", "Processing ADT data", "Writing H5MU files", "References", "Session Info" ], "created": "2021-12-10 02:16:06", "modified": "2022-01-10 14:31:59", "commits": 7 }, { "source": "Getting-Started.Rmd", "filename": "Getting-Started.html", "title": "Getting started with MuData for MultiAssayExperiment", "author": "Danila Bredikhin, Ilia Kats", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Loading libraries", "Writing H5MU files", "Reading H5MU files", "Creating MAE objects from H5MU files", "Backed objects", "References", "Session Info" ], "created": "2021-09-23 11:54:06", "modified": "2021-12-21 09:31:44", "commits": 7 } ], "_score": 7.092545207605606, "_indexed": true, "_nocasepkg": "mudata", "_universes": [ "bioc", "ilia-kats" ], "_previous": "1.17.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.1", "date": "2026-10-26T23:36:25.000Z", "distro": "resolute", "commit": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "fileid": "https://r2.ropensci.org/5fcb02ea122396e26a8cde180c6c6b9e35cf6ebca0270cc5f2def89898a8b17b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40419237663" }, { "r": "4.6.1", "os": "linux", "version": "1.17.1", "date": "2026-10-26T23:38:41.000Z", "distro": "resolute", "commit": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "fileid": "https://r2.ropensci.org/4a39a1a5634a8921f9439d3753eb79c498ff8ebe8f13a324e7b836b31428f24d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40419237663" }, { "r": "4.5.3", "os": "mac", "version": "1.17.1", "date": "2026-10-26T23:56:55.000Z", "commit": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "fileid": "https://r2.ropensci.org/8ba93fb337ae3527b7fd7554da151281ec7174bfd59501e4c4b07cb2ce1555b4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40419237663" }, { "r": "4.6.1", "os": "mac", "version": "1.17.1", "date": "2026-10-26T23:57:55.000Z", "commit": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "fileid": "https://r2.ropensci.org/78cff098fdfacc44622cb9e4effd0958ac8dcf2b6ab1b82aaf0bfc50c4b32fa9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40419237663" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.1", "date": "2026-10-26T23:37:58.000Z", "commit": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "fileid": "https://r2.ropensci.org/572bc72fd1d0e607bd68a32eab75dd3bc6766bc0eca48dabd62db03e8ae8d854", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40419237663" }, { "r": "4.7.0", "os": "win", "version": "1.17.1", "date": "2026-10-26T23:38:12.000Z", "commit": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "fileid": "https://r2.ropensci.org/f708f93375b768142f59fdeaa9c526e6979bdde09010eba24d79ec611f4ca0d3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40419237663" }, { "r": "4.5.3", "os": "win", "version": "1.17.1", "date": "2026-10-26T23:39:42.000Z", "commit": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "fileid": "https://r2.ropensci.org/23734b147cc90ccce84083f2f45a3a95922547e6e30da1d7b3bd5cd95a4acccb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40419237663" }, { "r": "4.6.1", "os": "win", "version": "1.17.1", "date": "2026-10-26T23:39:42.000Z", "commit": "d2deb40ed1170df68f2d3e9e764abf6f9dc8c2bc", "fileid": "https://r2.ropensci.org/0ae41155f3a839d7c446db01c500c55d2cdfe216a12165a68ed3ddfc63d4b70d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40419237663" } ] }