{ "_id": "6a4a0d1db9bf02698bd564a5", "Package": "tidyomics", "Title": "Easily install and load the tidyomics ecosystem", "Version": "1.9.0", "Authors@R": "c(\nperson(given = \"Stefano\",\nfamily = \"Mangiola\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mangiolastefano@gmail.com\",\ncomment = c(ORCID = \"0000-0001-7474-836X\")),\nperson(given = \"Michael\",\nfamily = \"Love\",\nrole = c(\"aut\"),\nemail = \"michaelisaiahlove@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8401-0545\")),\nperson(given = \"William\",\nfamily = \"Hutchison\",\nrole = c(\"aut\"),\nemail = \"hutchison.w@wehi.edu.au\",\ncomment = c(ORCID = \"0009-0001-6242-4269\"))\n)", "Description": "The tidyomics ecosystem is a set of packages for ’omic\ndata analysis that work together in harmony; they share common\ndata representations and API design, consistent with the\ntidyverse ecosystem. The tidyomics package is designed to make\nit easy to install and load core packages from the tidyomics\necosystem with a single command.", "License": "MIT + file LICENSE", "URL": "https://github.com/tidyomics/tidyomics", "BugReports": "https://github.com/tidyomics/tidyomics/issues", "VignetteBuilder": "knitr", "Biarch": "true", "biocViews": "AssayDomain, Infrastructure, RNASeq, DifferentialExpression,\nGeneExpression, Normalization, Clustering, QualityControl,\nSequencing, Transcription, Transcriptomics", "Config/testthat/edition": "3", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libglpk-dev make libmagick++-dev gsfonts\nlibbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev python3 xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:02:22 UTC", "RemoteUrl": "https://github.com/bioc/tidyomics", "RemoteRef": "HEAD", "RemoteSha": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-10 06:45:35 UTC", "User": "root" }, "Author": "Stefano Mangiola [aut, cre] (ORCID:\n),\nMichael Love [aut] (ORCID: ),\nWilliam Hutchison [aut] (ORCID:\n)", "Maintainer": "Stefano Mangiola ", "_user": "bioc", "_type": "src", "_file": "tidyomics_1.9.0.tar.gz", "_fileid": "https://r2.ropensci.org/8d96b3a95e875ef319a2e0bfec56dab2e8b2e1af73d8c7be30fc4bbc4ae33726", "_filesize": 136745, "_sha256": "8d96b3a95e875ef319a2e0bfec56dab2e8b2e1af73d8c7be30fc4bbc4ae33726", "_expires": "2026-10-13T07:51:55.000Z", "_created": "2026-06-10T06:45:35.000Z", "_published": "2026-07-05T07:51:57.100Z", "_bioccheck": { "error": 1, "warning": 2, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27258200332", "_status": "success", "_upstream": "https://github.com/bioc/tidyomics", "_commit": { "id": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381342 }, "_maintainer": { "name": "Stefano Mangiola", "email": "mangiolastefano@gmail.com", "login": "stemangiola", "twitter": "@steman_research", "description": "", "uuid": 7232890, "orcid": "0000-0001-7474-836X" }, "_distro": "noble", "_jobs": [ { "job": 85204547423, "time": 238, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7528494097" }, { "job": 85204547320, "time": 421, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7528543786" }, { "job": 85204547572, "time": 348, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7528523684" }, { "job": 85204547638, "time": 298, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7528512007" }, { "job": 85204547404, "time": 258, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7528500889" }, { "job": 85204547358, "time": 365, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7528427226" }, { "job": 85204547367, "time": 191, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7528481244" }, { "job": 85204547383, "time": 310, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7528514420" }, { "job": 85204547619, "time": 288, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7528508707" }, { "job": 85204547445, "time": 252, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7528497789" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "tidySummarizedExperiment", "role": "Imports" }, { "package": "tidySingleCellExperiment", "role": "Imports" }, { "package": "tidySpatialExperiment", "role": "Imports" }, { "package": "tidyseurat", "role": "Imports" }, { "package": "plyranges", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "utils", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "mockr", "version": ">= 0.2.0", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.41", "role": "Suggests" }, { "package": "rmarkdown", "version": ">= 2.20", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.1.6", "role": "Suggests" }, { "package": "nullranges", "role": "Suggests" }, { "package": "tidybulk", "role": "Suggests" }, { "package": "plyinteractions", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-42", "n": 1 }, { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 4 }, { "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": [ "assaydomain", "infrastructure", "rnaseq", "differentialexpression", "geneexpression", "normalization", "clustering", "qualitycontrol", "sequencing", "transcription", "transcriptomics", "cytometry", "genomics", "tidyverse" ], "_stars": 75, "_contributors": [ { "user": "william-hutchison", "count": 53, "uuid": 88420272 }, { "user": "stemangiola", "count": 25, "uuid": 7232890 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "mikelove", "count": 1, "uuid": 69203 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 260, "source": "https://www.bioconductor.org/packages/stats/bioc/tidyomics" }, "_devurl": "https://github.com/tidyomics/tidyomics", "_searchresults": 19, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/tidyomics.html", "manual.pdf" ], "_homeurl": "https://github.com/tidyomics/tidyomics", "_realowner": "bioc", "_cranurl": false, "_exports": [ "tidyomics", "tidyomics_conflicts", "tidyomics_packages" ], "_help": [ { "page": "tidyomics", "title": "tidyomics", "topics": [ "tidyomics" ] }, { "page": "tidyomics_conflicts", "title": "Conflicts between the tidyomics and other packages", "topics": [ "tidyomics_conflicts" ] }, { "page": "tidyomics_packages", "title": "List all packages loaded by the tidyomics metapackage", "topics": [ "tidyomics_packages" ] } ], "_pkglogo": "https://github.com/bioc/tidyomics/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/tidyomics/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "cachem", "caTools", "cigarillo", "cli", "cluster", "codetools", "commonmark", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "deldir", "digest", "dotCall64", "dplyr", "dqrng", "ellipsis", "evaluate", "fansi", "farver", "fastDummies", "fastmap", "filelock", "fitdistrplus", "FNN", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "future", "future.apply", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "ggrepel", "ggridges", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "ica", "igraph", "IRanges", "irlba", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lmtest", "magick", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "miniUI", "nlme", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pillar", "pkgconfig", "plotly", "plyr", "plyranges", "plyxp", "png", "polyclip", "progressr", "promises", "purrr", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppProgress", "RcppTOML", "RCurl", "reshape2", "restfulr", "reticulate", "Rhtslib", "rjson", "rlang", "rmarkdown", "ROCR", "rprojroot", "Rsamtools", "RSpectra", "RSQLite", "rtracklayer", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scattermore", "sctransform", "Seqinfo", "Seurat", "SeuratObject", "shiny", "SingleCellExperiment", "sitmo", "snow", "sourcetools", "sp", "spam", "SparseArray", "SpatialExperiment", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tensor", "tibble", "tidygate", "tidyr", "tidyselect", "tidyseurat", "tidySingleCellExperiment", "tidySpatialExperiment", "tidySummarizedExperiment", "tinytex", "ttservice", "utf8", "uwot", "vctrs", "viridis", "viridisLite", "withr", "xfun", "XML", "xtable", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "loading-tidyomics.Rmd", "filename": "loading-tidyomics.html", "title": "Loading the tidyomics ecosystem", "author": "William Hutchison", "engine": "knitr::knitr", "headings": [ "Overview", "The tidyomics ecosystem", "Core packages", "Additional manipulation packages", "Analysis packages", "Installation", "Loading the tidyomics ecosystem" ], "created": "2024-01-04 22:42:20", "modified": "2025-10-26 09:06:33", "commits": 5 } ], "_score": 6.931966114728173, "_indexed": true, "_nocasepkg": "tidyomics", "_universes": [ "bioc", "stemangiola", "tidyomics" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.9.0", "date": "2026-06-10T06:50:16.000Z", "distro": "noble", "commit": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "fileid": "https://r2.ropensci.org/53060ed912f44cafc1fb130a4b65fe91683117bcfcad4e06207d3c47350371bc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258200332" }, { "r": "4.6.0", "os": "linux", "version": "1.9.0", "date": "2026-06-10T06:49:26.000Z", "distro": "noble", "commit": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "fileid": "https://r2.ropensci.org/e46c10d8ca353b5e44dff281c928c3fd828ba1b795eb68b42eb3794032d09d38", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258200332" }, { "r": "4.5.3", "os": "mac", "version": "1.9.0", "date": "2026-06-10T06:48:45.000Z", "commit": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "fileid": "https://r2.ropensci.org/c6355a284241c70f665703e2805c823fcac337babeaadd51c35d0301f9fecca9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258200332" }, { "r": "4.6.0", "os": "mac", "version": "1.9.0", "date": "2026-06-10T06:47:59.000Z", "commit": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "fileid": "https://r2.ropensci.org/a8079c6a204fab44a119df28ec7b0c8d5b2634a96821d96ad5112c31a27bfe76", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258200332" }, { "r": "4.6.0", "os": "wasm", "version": "1.9.0", "date": "2026-06-10T06:49:27.000Z", "commit": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "fileid": "https://r2.ropensci.org/e9deb2420070ed59a3c5ee3934d1af5fbf120952899864f680a9cf1c0396451f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258200332" }, { "r": "4.7.0", "os": "win", "version": "1.9.0", "date": "2026-06-10T06:48:27.000Z", "commit": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "fileid": "https://r2.ropensci.org/e13f15430fca1a99200e63bfa64bd0b9eef39eed537f67547b59106f47431b01", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258200332" }, { "r": "4.5.3", "os": "win", "version": "1.9.0", "date": "2026-06-10T06:48:03.000Z", "commit": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "fileid": "https://r2.ropensci.org/d2732e79dbab28e3822c9854e89d7adfe7cdcfde855d06a807bd59904156b3ac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258200332" }, { "r": "4.6.0", "os": "win", "version": "1.9.0", "date": "2026-06-10T06:47:38.000Z", "commit": "a7fbe5a3f6ceb70a04b5a0dd105b5ec541b5d8e2", "fileid": "https://r2.ropensci.org/22e8cd5bed71b8d78f76bf715a6950e8ed7fd8c52d20fa7738f46392faa41791", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27258200332" } ] }