{ "_id": "6a2cf8283efcd9bda42e4f8b", "Package": "MicrobiomeBenchmarkData", "Title": "Datasets for benchmarking in microbiome research", "Version": "1.15.1", "Description": "The MicrobiomeBenchmarkData package provides functionality\nto access microbiome datasets suitable for benchmarking. These\ndatasets have some biological truth, which allows to have\nexpected results for comparison. The datasets come from various\npublished sources and are provided as TreeSummarizedExperiment\nobjects. Currently, only datasets suitable for benchmarking\ndifferential abundance methods are available.", "Authors@R": "c(\nperson(\"Samuel\", \"Gamboa\", , \"Samuel.Gamboa.Tuz@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6863-7943\")),\nperson(\"Levi\", \"Waldron\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-2725-0694\")),\nperson(\"Marcel\", \"Ramos\", role = \"ctb\"),\nperson(\"NCI\", role = \"fnd\",\ncomment = c(GrantNo. = \"R01CA230551\"))\n)", "License": "Artistic-2.0", "LazyData": "false", "biocViews": "ExperimentData, MicrobiomeData, ReproducibleResearch,\nSequencingData", "BugReports": "https://github.com/waldronlab/MicrobiomeBenchmarkData/issues", "URL": "https://github.com/waldronlab/MicrobiomeBenchmarkData,\nhttp://waldronlab.io/MicrobiomeBenchmarkData/", "BiocType": "ExperimentData", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev", "Repository": "https://waldronlab.r-universe.dev", "Date/Publication": "2026-04-29 20:51:01 UTC", "RemoteUrl": "https://github.com/waldronlab/MicrobiomeBenchmarkData", "RemoteRef": "HEAD", "RemoteSha": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-13 06:20:08 UTC", "User": "root" }, "Author": "Samuel Gamboa [aut, cre] (ORCID:\n),\nLevi Waldron [aut] (ORCID: ),\nMarcel Ramos [ctb],\nNCI [fnd] (GrantNo.: R01CA230551)", "Maintainer": "Samuel Gamboa ", "MD5sum": "198ad69affdb3506fb25147323f91818", "_user": "waldronlab", "_type": "src", "_file": "MicrobiomeBenchmarkData_1.15.1.tar.gz", "_fileid": "77b3a322232d3a0784b92c531404c17f0d8b99f29f232cbbbbe782038920a03b", "_filesize": 182050, "_sha256": "77b3a322232d3a0784b92c531404c17f0d8b99f29f232cbbbbe782038920a03b", "_created": "2026-06-13T06:20:08.000Z", "_published": "2026-06-13T06:26:48.552Z", "_distro": "noble", "_jobs": [ { "job": 81168689453, "time": 346, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7608145113" }, { "job": 81168689452, "time": 329, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7608143664" }, { "job": 81168689466, "time": 201, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7608128378" }, { "job": 81168689460, "time": 207, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7608128423" }, { "job": 81168316358, "time": 349, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7608101789" }, { "job": 81168689448, "time": 164, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7608123644" }, { "job": 81168689476, "time": 285, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7608137797" }, { "job": 81168689473, "time": 280, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7608137432" }, { "job": 81168689467, "time": 256, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7608134365" } ], "_buildurl": "https://github.com/r-universe/waldronlab/actions/runs/27458796058", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/waldronlab/MicrobiomeBenchmarkData", "_commit": { "id": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "author": "LiNk-NY ", "committer": "LiNk-NY ", "message": "version bump 1.15.1\n", "time": 1777495861 }, "_maintainer": { "name": "Samuel Gamboa", "email": "samuel.gamboa.tuz@gmail.com", "login": "sdgamboa", "orcid": "0000-0002-6863-7943", "description": "\n", "uuid": 53412049 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "TreeSummarizedExperiment", "role": "Depends" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "mia", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "magrittr", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "purrr", "role": "Suggests" } ], "_owner": "waldronlab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 4 } ], "_tags": [], "_topics": [ "experimentdata", "microbiomedata", "reproducibleresearch", "sequencingdata", "bioconductor-package", "r01ca230551" ], "_stars": 0, "_contributors": [ { "user": "sdgamboa", "count": 127, "uuid": 53412049 }, { "user": "hpages", "count": 8, "uuid": 8810451 }, { "user": "lshep", "count": 8, "uuid": 18724380 }, { "user": "link-ny", "count": 3, "uuid": 4392950 } ], "_userbio": { "uuid": 15236403, "type": "organization", "name": "Waldron Lab at the CUNY SPH", "description": "Software and educational materials from the Waldron lab for computational biostatistics at the CUNY SPH in New York City" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MicrobiomeBenchmarkData" }, "_devurl": "https://github.com/waldronlab/microbiomebenchmarkdata", "_pkgdown": "http://waldronlab.io/MicrobiomeBenchmarkData/", "_searchresults": 19, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MicrobiomeBenchmarkData.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "getBenchmarkData", "removeCache", "scml" ], "_datasets": [ { "name": "sampleMetadata", "title": "sampleMetadata", "object": "sampleMetadata", "file": "sampleMetadata.rda", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "dataset", "sample_id", "subject_id", "visit_number", "gender", "run_center", "body_site", "body_subsite", "ncbi_accession", "library_size", "sequencing_platform", "pmid", "study_condition", "disease", "sequencing_method", "variable_region_16s", "age", "age_category", "country", "non_westernized", "DNA_extraction_kit", "PMID", "number_reads", "number_bases", "minimum_read_length", "median_read_length", "NCBI_accession", "curator", "BMI", "description", "ethnicity", "ph", "nugent_score", "nugent_score_category", "community_group" ], "rows": 1125, "table": true, "tojson": true } ], "_help": [ { "page": "getBenchmarkData", "title": "Get dataset", "topics": [ "getBenchmarkData" ] }, { "page": "MicrobiomeBenchmarkData", "title": "MicrobiomeBenchmarkData", "topics": [ "MicrobiomeBenchmarkData-package", "MicrobiomeBenchmarkData" ] }, { "page": "removeCache", "title": "Remove cache", "topics": [ "removeCache" ] }, { "page": "sampleMetadata", "title": "sampleMetadata", "topics": [ "sampleMetadata" ] }, { "page": "scml", "title": "SCML: spike-in-based calibration to total microbial load", "topics": [ "scml" ] } ], "_readme": "https://github.com/waldronlab/MicrobiomeBenchmarkData/raw/HEAD/README.md", "_rundeps": [ "abind", "ape", "askpass", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "digest", "dplyr", "fastmap", "filelock", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "glue", "httr2", "IRanges", "jsonlite", "lambda.r", "lattice", "lazyeval", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "nlme", "openssl", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "Rcpp", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tidytree", "treeio", "TreeSummarizedExperiment", "utf8", "vctrs", "withr", "XVector", "yulab.utils" ], "_vignettes": [ { "source": "datasets.Rmd", "filename": "datasets.html", "title": "Datasets in MicrobiomeBenchmarkData", "author": "Samuel Gamboa", "engine": "knitr::rmarkdown", "headings": [], "created": "2021-09-24 18:48:52", "modified": "2022-10-26 16:11:01", "commits": 16 }, { "source": "MicrobiomeBenchmarkData.Rmd", "filename": "MicrobiomeBenchmarkData.html", "title": "MicrobiomeBenchmarkData", "author": "Samuel Gamboa, Levi Waldron", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Sample metadata", "Accessing datasets", "Print avaialable datasets", "Access a single dataset", "Access a few datasets", "Access all of the datasets", "Annotations for each taxa are included in rowData", "Cache", "Session information" ], "created": "2021-09-07 17:27:05", "modified": "2022-10-26 16:11:01", "commits": 21 }, { "source": "recalibrare_spikein_data.Rmd", "filename": "recalibrare_spikein_data.html", "title": "Recalibration of the Stammler_2016_16S_spikein dataset", "author": "Samuel D. Gamboa-Tuz", "engine": "knitr::rmarkdown", "headings": [ "Import data", "Ids of the spike-in bacteria", "Recalibrate based on Salinibacter ruber abundance.", "A more convenient way using the scml function included in the package:", "Session information" ], "created": "2022-07-06 05:17:27", "modified": "2024-09-02 23:13:45", "commits": 7 } ], "_score": 4.232996110392154, "_indexed": true, "_nocasepkg": "microbiomebenchmarkdata", "_universes": [ "waldronlab", "sdgamboa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.15.1", "date": "2026-06-13T06:23:32.000Z", "distro": "noble", "commit": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "fileid": "1b2f2038d0b315d8bba00fbe7ce5d8cb846b04f9446eee74d2943aeee0c4144f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/27458796058" }, { "r": "4.6.0", "os": "linux", "version": "1.15.1", "date": "2026-06-13T06:23:31.000Z", "distro": "noble", "commit": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "fileid": "97b193be133e4fb95c97dfc59ae49f5bc1e2b318feb3dc1d64304c153d6e79b6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/27458796058" }, { "r": "4.5.3", "os": "mac", "version": "1.15.1", "date": "2026-06-13T06:22:28.000Z", "commit": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "fileid": "c0888837a9b07a635ea99e93af809e33d651368d3e6d80e035e2ebd4e950613a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/27458796058" }, { "r": "4.6.0", "os": "mac", "version": "1.15.1", "date": "2026-06-13T06:22:14.000Z", "commit": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "fileid": "6236787e6523fe7a65ac20e7945729c795c5c8413f4184c16f755e72734eebfa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/27458796058" }, { "r": "4.6.0", "os": "wasm", "version": "1.15.1", "date": "2026-06-13T06:23:33.000Z", "commit": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "fileid": "e96fbf5be041daac84eca4698097e1365b33b64712beb1c17f7e65b625d18c9f", "status": "success", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/27458796058" }, { "r": "4.7.0", "os": "win", "version": "1.15.1", "date": "2026-06-13T06:22:29.000Z", "commit": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "fileid": "fdd7d2287f853518c9112728efa59ca7208792efc274087cfbfd5673c07f2692", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/27458796058" }, { "r": "4.5.3", "os": "win", "version": "1.15.1", "date": "2026-06-13T06:22:23.000Z", "commit": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "fileid": "c3942726f496ee57c52497485e6962ec666ccf05794800c6649497ac0ae4f182", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/27458796058" }, { "r": "4.6.0", "os": "win", "version": "1.15.1", "date": "2026-06-13T06:21:59.000Z", "commit": "ed900aa65c5c5000f27d41236eb51fada07d72e7", "fileid": "d40be395e67b0fc062d600345ec229fcc79ebbdba04bebe1fc66d8ca42e97c20", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/waldronlab/actions/runs/27458796058" } ] }