{ "_id": "6a494edcf6c47c441949a3f0", "Package": "MGnifyR", "Type": "Package", "Version": "1.9.0", "Authors@R": "c(person(given = \"Tuomas\", family = \"Borman\", role = c(\"aut\", \"cre\"),\nemail = \"tuomas.v.borman@utu.fi\",\ncomment = c(ORCID = \"0000-0002-8563-8884\")),\nperson(given = \"Ben\", family = \"Allen\", role = c(\"aut\"),\nemail = \"ben.allen@ncl.ac.uk\"),\nperson(given = \"Leo\", family = \"Lahti\", role = c(\"aut\"),\nemail = \"leo.lahti@iki.fi\",\ncomment = c(ORCID = \"0000-0001-5537-637X\")))", "Title": "R interface to EBI MGnify metagenomics resource", "Description": "Utility package to facilitate integration and analysis of\nEBI MGnify data in R. The package can be used to import\nmicrobial data for instance into TreeSummarizedExperiment\n(TreeSE). In TreeSE format, the data is directly compatible\nwith miaverse framework.", "biocViews": "Infrastructure, DataImport, Metagenomics, Microbiome,\nMicrobiomeData", "License": "Artistic-2.0 | file LICENSE", "Encoding": "UTF-8", "URL": "https://github.com/EBI-Metagenomics/MGnifyR", "BugReports": "https://github.com/EBI-Metagenomics/MGnifyR/issues", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Collate": "'utils.R' 'MgnifyClient.R' 'AllGenerics.R' 'AllClasses.R'\n'AllAccessors.R' 'MGnifyR.R' 'deprecate.R' 'doQuery.R'\n'getData.R' 'getFile.R' 'getMetadata.R' 'getResult.R'\n'searchAnalysis.R'", "Config/pak/sysreqs": "cmake libglpk-dev make libgsl0-dev libicu-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:02:42 UTC", "RemoteUrl": "https://github.com/bioc/MGnifyR", "RemoteRef": "HEAD", "RemoteSha": "8023712cff8200373de29e90dd5077861d36015a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 12:14:11 UTC", "User": "root" }, "Author": "Tuomas Borman [aut, cre] (ORCID:\n),\nBen Allen [aut],\nLeo Lahti [aut] (ORCID: )", "Maintainer": "Tuomas Borman ", "_user": "bioc", "_type": "src", "_file": "MGnifyR_1.9.0.tar.gz", "_fileid": "https://r2.ropensci.org/cb5e4fbd4615baabb9a343a74ffc2364c6c7f2545692ba3b4ed4bbeb317df8f0", "_filesize": 4021082, "_sha256": "cb5e4fbd4615baabb9a343a74ffc2364c6c7f2545692ba3b4ed4bbeb317df8f0", "_expires": "2026-10-12T18:20:09.000Z", "_created": "2026-07-03T12:14:11.000Z", "_published": "2026-07-04T18:20:12.285Z", "_bioccheck": { "error": 1, "warning": 5, "note": 9 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28659614504", "_status": "success", "_upstream": "https://github.com/bioc/MGnifyR", "_commit": { "id": "8023712cff8200373de29e90dd5077861d36015a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381362 }, "_maintainer": { "name": "Tuomas Borman", "email": "tuomas.v.borman@utu.fi", "orcid": "0000-0002-8563-8884" }, "_distro": "resolute", "_jobs": [ { "job": 85155752429, "time": 234, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8078559884" }, { "job": 85155752386, "time": 891, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8066499074" }, { "job": 85155752394, "time": 930, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8066511905" }, { "job": 85155752403, "time": 690, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8078633137" }, { "job": 85155752505, "time": 693, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8066477214" }, { "job": 85155752192, "time": 306, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8066205119" }, { "job": 85155752337, "time": 207, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8066275114" }, { "job": 85155752381, "time": 845, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8066484191" }, { "job": 85155752483, "time": 823, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8066475102" }, { "job": 85155752376, "time": 785, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8066462071" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "MultiAssayExperiment", "role": "Depends" }, { "package": "TreeSummarizedExperiment", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "BiocGenerics", "role": "Depends" }, { "package": "mia", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "urltools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "biomformat", "role": "Suggests" }, { "package": "broom", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "miaViz", "role": "Suggests" }, { "package": "vegan", "role": "Suggests" }, { "package": "scater", "role": "Suggests" }, { "package": "phyloseq", "role": "Suggests" }, { "package": "magick", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-42", "n": 1 }, { "week": "2026-02", "n": 3 }, { "week": "2026-07", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "dataimport", "metagenomics", "microbiome", "microbiomedata" ], "_stars": 23, "_contributors": [ { "user": "tuomasborman", "count": 61, "uuid": 60338854 }, { "user": "beadyallen", "count": 43, "uuid": 4439410 }, { "user": "antagomir", "count": 20, "uuid": 1228382 }, { "user": "jwokaty", "count": 8, "uuid": 1744257 }, { "user": "artur-sannikov", "count": 1, "uuid": 40318410 }, { "user": "hpages", "count": 1, "uuid": 8810451 }, { "user": "0xmuluh", "count": 1, "uuid": 127390183 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/ebi-metagenomics/mgnifyr", "_searchresults": 43, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MGnifyR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/ebi-metagenomics/mgnifyr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "authTok", "authTok<-", "cacheDir", "cacheDir<-", "clearCache", "clearCache<-", "databaseUrl", "databaseUrl<-", "doQuery", "getData", "getFile", "getMetadata", "getResult", "mgnify_analyses_from_samples", "mgnify_analyses_from_studies", "mgnify_client", "mgnify_download", "mgnify_get_analyses_metadata", "mgnify_get_analyses_phyloseq", "mgnify_get_analyses_results", "mgnify_get_download_urls", "mgnify_query", "mgnify_retrieve_json", "MgnifyClient", "searchAnalysis", "searchFile", "showWarnings", "showWarnings<-", "useCache", "useCache<-", "verbose", "verbose<-" ], "_help": [ { "page": "MGnifyR-package", "title": "'MGnifyR' Package.", "topics": [ "MGnifyR-package", "MGnifyR" ] }, { "page": "MgnifyClient-accessors", "title": "MgnifyClient accessors and mutators", "topics": [ "authTok", "authTok,MgnifyClient-method", "authTok<-", "authTok<-,MgnifyClient-method", "cacheDir", "cacheDir,MgnifyClient-method", "cacheDir<-", "cacheDir<-,MgnifyClient-method", "clearCache", "clearCache,MgnifyClient-method", "clearCache<-", "clearCache<-,MgnifyClient-method", "databaseUrl", "databaseUrl,MgnifyClient-method", "databaseUrl<-", "databaseUrl<-,MgnifyClient-method", "MgnifyClient-accessors", "showWarnings", "showWarnings,MgnifyClient-method", "showWarnings<-", "showWarnings<-,MgnifyClient-method", "useCache", "useCache,MgnifyClient-method", "useCache<-", "useCache<-,MgnifyClient-method", "verbose", "verbose,MgnifyClient-method", "verbose<-", "verbose<-,MgnifyClient-method" ] }, { "page": "deprecate", "title": "These functions will be deprecated. Please use other functions instead.", "topics": [ "deprecate", "mgnify_analyses_from_samples", "mgnify_analyses_from_studies", "mgnify_client", "mgnify_download", "mgnify_get_analyses_metadata", "mgnify_get_analyses_phyloseq", "mgnify_get_analyses_results", "mgnify_get_download_urls", "mgnify_query", "mgnify_retrieve_json" ] }, { "page": "doQuery", "title": "Search MGnify database for studies, samples, runs, analyses, biomes, assemblies, and genomes.", "topics": [ "doQuery", "doQuery,MgnifyClient-method" ] }, { "page": "getData", "title": "Versatile function to retrieve raw results", "topics": [ "getData", "getData,MgnifyClient-method" ] }, { "page": "getFile", "title": "Download any MGnify files, also including processed reads and identified protein sequences", "topics": [ "getFile", "getFile,MgnifyClient-method", "searchFile", "searchFile,MgnifyClient-method" ] }, { "page": "getMetadata", "title": "Get all study, sample and analysis metadata for the supplied analysis accessions", "topics": [ "getMetadata", "getMetadata,MgnifyClient-method" ] }, { "page": "getResult", "title": "Get microbial and/or functional profiling data for a list of accessions", "topics": [ "getResult", "getResult,MgnifyClient-method" ] }, { "page": "MgnifyClient", "title": "Constructor for creating a MgnifyClient object to allow the access to MGnify database.", "topics": [ "MgnifyClient", "MgnifyClient-class" ] }, { "page": "searchAnalysis", "title": "Look up analysis accession IDs for one or more study or sample accessions", "topics": [ "searchAnalysis", "searchAnalysis,MgnifyClient-method" ] } ], "_readme": "https://github.com/bioc/MGnifyR/raw/HEAD/README.md", "_rundeps": [ "abind", "ape", "askpass", "assorthead", "beachmat", "beeswarm", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "Biostrings", "bluster", "cli", "cluster", "codetools", "cpp11", "crayon", "curl", "DBI", "DECIPHER", "decontam", "DelayedArray", "DelayedMatrixStats", "digest", "DirichletMultinomial", "dplyr", "dqrng", "ecodive", "farver", "FNN", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggbeeswarm", "ggplot2", "ggrepel", "glue", "gridExtra", "gtable", "httr", "igraph", "IRanges", "irlba", "isoband", "jsonlite", "labeling", "lambda.r", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mgcv", "mia", "mime", "MultiAssayExperiment", "nlme", "openssl", "permute", "pheatmap", "pillar", "pkgconfig", "plyr", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppEigen", "RcppML", "RcppProgress", "reshape2", "rlang", "RSpectra", "rsvd", "Rtsne", "S4Arrays", "S4Vectors", "S7", "ScaledMatrix", "scales", "scater", "scuttle", "Seqinfo", "SingleCellExperiment", "sitmo", "snow", "SparseArray", "sparseMatrixStats", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tidytree", "treeio", "TreeSummarizedExperiment", "triebeard", "urltools", "utf8", "uwot", "vctrs", "vegan", "vipor", "viridis", "viridisLite", "withr", "XVector", "yulab.utils" ], "_vignettes": [ { "source": "MGnifyR.Rmd", "filename": "MGnifyR.html", "title": "MGnifyR", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Load MGnifyR package", "Create a client", "Functions for fetching the data", "Search data", "Find relevent analyses accessions", "Fetch metadata", "Fetch microbiome data", "Fetch raw files", "Fetch sequence files" ], "created": "2020-09-11 11:09:34", "modified": "2024-09-25 17:22:53", "commits": 16 }, { "source": "MGnify_course.Rmd", "filename": "MGnify_course.html", "title": "Metagenomics bioinformatics at MGnify", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Load packages", "Data import", "Preprocessing", "Alpha diversity", "Beta diversity", "Differential abundance analysis (DAA)", "Session info" ], "created": "2024-09-25 17:22:53", "modified": "2024-09-26 07:55:17", "commits": 2 }, { "source": "MGnifyR_long.Rmd", "filename": "MGnifyR_long.html", "title": "MGnifyR, extended vignette", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Load MGnifyR package", "Create a client", "Functions for fetching the data", "Search data", "Find relevent analyses accessions", "Fetch metadata", "Fetch microbiome data", "Amplicon sequencing", "Metagenomics", "Fetch raw files", "Fetch sequence files" ], "created": "2023-10-30 13:05:00", "modified": "2024-09-25 17:22:53", "commits": 9 } ], "_score": 7.551498792364467, "_indexed": true, "_nocasepkg": "mgnifyr", "_universes": [ "bioc", "ebi-metagenomics" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.9.0", "date": "2026-07-03T12:18:25.000Z", "distro": "resolute", "commit": "8023712cff8200373de29e90dd5077861d36015a", "fileid": "https://r2.ropensci.org/fc5a8ebdfa275827702f111041d12d767484b3536010492e1ef51ad70242bb9a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659614504" }, { "r": "4.6.1", "os": "linux", "version": "1.9.0", "date": "2026-07-03T12:18:57.000Z", "distro": "resolute", "commit": "8023712cff8200373de29e90dd5077861d36015a", "fileid": "https://r2.ropensci.org/89e0a2328ecebcb5cd92518a7ca61ea148acea061e78b329f83bc4c8bd3d5be5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659614504" }, { "r": "4.5.3", "os": "mac", "version": "1.9.0", "date": "2026-07-04T05:12:27.000Z", "commit": "8023712cff8200373de29e90dd5077861d36015a", "fileid": "https://r2.ropensci.org/8a320f77839cdd7b1a5db1b66ab094185bbeaa4d526e97e5b83b90964e565f33", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659614504" }, { "r": "4.6.1", "os": "mac", "version": "1.9.0", "date": "2026-07-03T12:18:31.000Z", "commit": "8023712cff8200373de29e90dd5077861d36015a", "fileid": "https://r2.ropensci.org/2d4308c5cd4218d10574eab56c81da57c98e69e84512e5bb0a24f66770d7a574", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659614504" }, { "r": "4.6.0", "os": "wasm", "version": "1.9.0", "date": "2026-07-03T12:18:17.000Z", "commit": "8023712cff8200373de29e90dd5077861d36015a", "fileid": "https://r2.ropensci.org/97dace1b55370388afa3ba12a63b4df77ecc8e89df6542064090060c888f2875", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659614504" }, { "r": "4.7.0", "os": "win", "version": "1.9.0", "date": "2026-07-03T12:17:19.000Z", "commit": "8023712cff8200373de29e90dd5077861d36015a", "fileid": "https://r2.ropensci.org/ebb324d6368d824c591791b5efffc3ed83ecf657bff6bcead1e6f90885d3a7db", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659614504" }, { "r": "4.5.3", "os": "win", "version": "1.9.0", "date": "2026-07-03T12:16:46.000Z", "commit": "8023712cff8200373de29e90dd5077861d36015a", "fileid": "https://r2.ropensci.org/668955e4292b46a1f92528d1563157571b13dee8fa2ccfe237379260047a82e6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659614504" }, { "r": "4.6.1", "os": "win", "version": "1.9.0", "date": "2026-07-03T12:16:28.000Z", "commit": "8023712cff8200373de29e90dd5077861d36015a", "fileid": "https://r2.ropensci.org/1e24680d1baf61b6a6dfa79c0de1374596f50b7aa266397e462b26c3a070dc85", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659614504" } ] }