{
  "_id": "6a19668aacfb0bcc41de75cc",
  "Package": "CellBench",
  "Type": "Package",
  "Title": "Construct Benchmarks for Single Cell Analysis Methods",
  "Version": "1.29.0",
  "Authors@R": "c(\nperson(\"Shian\", \"Su\", email = \"su.s@wehi.edu.au\", role = c(\"cre\", \"aut\")),\nperson(\"Saskia\", \"Freytag\", role = \"aut\"),\nperson(\"Luyi\", \"Tian\", role = \"aut\"),\nperson(\"Xueyi\", \"Dong\", role = \"aut\"),\nperson(\"Matthew\", \"Ritchie\", role = \"aut\"),\nperson(\"Peter\", \"Hickey\", role = \"ctb\"),\nperson(\"Stuart\", \"Lee\", role = \"ctb\"))",
  "Description": "This package contains infrastructure for benchmarking\nanalysis methods and access to single cell mixture benchmarking\ndata. It provides a framework for organising analysis methods\nand testing combinations of methods in a pipeline without\nexplicitly laying out each combination. It also provides\nutilities for sampling and filtering SingleCellExperiment\nobjects, constructing lists of functions with varying\nparameters, and multithreaded evaluation of analysis methods.",
  "biocViews": "Software, Infrastructure, SingleCell",
  "URL": "https://github.com/shians/cellbench",
  "BugReports": "https://github.com/Shians/CellBench/issues",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "libicu-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:41 UTC",
  "RemoteUrl": "https://github.com/bioc/CellBench",
  "RemoteRef": "HEAD",
  "RemoteSha": "1afd28752fe95dd818da1b0e61de197e5617dff5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 08:27:36 UTC",
    "User": "root"
  },
  "Author": "Shian Su [cre, aut],\nSaskia Freytag [aut],\nLuyi Tian [aut],\nXueyi Dong [aut],\nMatthew Ritchie [aut],\nPeter Hickey [ctb],\nStuart Lee [ctb]",
  "Maintainer": "Shian Su <su.s@wehi.edu.au>",
  "MD5sum": "8a9d650bd4d143084007c6f585e2f405",
  "_user": "bioc",
  "_type": "src",
  "_file": "CellBench_1.29.0.tar.gz",
  "_fileid": "be826bb45cc752adb2817c0ea016e85620ec3fba4d73c7514668f8b5e1a7cadf",
  "_filesize": 2253547,
  "_sha256": "be826bb45cc752adb2817c0ea016e85620ec3fba4d73c7514668f8b5e1a7cadf",
  "_created": "2026-05-29T08:27:36.000Z",
  "_published": "2026-05-29T10:12:26.265Z",
  "_jobs": [
    {
      "job": 78465532323,
      "time": 191,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7286477541"
    },
    {
      "job": 78465532249,
      "time": 301,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286510437"
    },
    {
      "job": 78465532336,
      "time": 339,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286522717"
    },
    {
      "job": 78465532270,
      "time": 231,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7288286096"
    },
    {
      "job": 78465532303,
      "time": 232,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7288287080"
    },
    {
      "job": 78464828323,
      "time": 291,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286421432"
    },
    {
      "job": 78465532281,
      "time": 148,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286464647"
    },
    {
      "job": 78465532309,
      "time": 299,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286510033"
    },
    {
      "job": 78465532421,
      "time": 279,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7286503064"
    },
    {
      "job": 78465532300,
      "time": 241,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286492131"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26626603621",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/CellBench",
  "_commit": {
    "id": "1afd28752fe95dd818da1b0e61de197e5617dff5",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380581
  },
  "_maintainer": {
    "name": "Shian Su",
    "email": "su.s@wehi.edu.au",
    "login": "shians",
    "description": "Bioinformatician with an interest in high-throughput genomics and epigenomics. Experienced in R and C++.",
    "uuid": 6036662
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Depends"
    },
    {
      "package": "magrittr",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "tibble",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Depends"
    },
    {
      "package": "assertthat",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocFileCache",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "memoise",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "version": ">= 0.3.0",
      "role": "Imports"
    },
    {
      "package": "rappdirs",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "lubridate",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-42",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "infrastructure",
    "singlecell",
    "benchmark",
    "bioinformatics"
  ],
  "_stars": 32,
  "_contributors": [
    {
      "user": "shians",
      "count": 338,
      "uuid": 6036662
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "petehaitch",
      "count": 1,
      "uuid": 1049741
    },
    {
      "user": "qgouil",
      "count": 1,
      "uuid": 13610297
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 451,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CellBench"
  },
  "_mentions": 7,
  "_devurl": "https://github.com/shians/cellbench",
  "_searchresults": 113,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/CellBench.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/shians/cellbench",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "all_unique",
    "any_task_errors",
    "apply_methods",
    "apply_metrics",
    "arrow_sep",
    "as_pipeline_list",
    "begin_benchmark",
    "cache_method",
    "cellbench_case_study",
    "cellbench_file",
    "clear_cached_datasets",
    "clear_cellbench_cache",
    "collapse_pipeline",
    "data_list",
    "filter_zero_genes",
    "fn_arg_seq",
    "fn_list",
    "is_all_of",
    "is_one_of",
    "is.task_error",
    "keep_high_count_cells",
    "keep_high_count_genes",
    "keep_high_var_genes",
    "load_all_data",
    "load_cell_mix_data",
    "load_mrna_mix_data",
    "load_sc_data",
    "mhead",
    "pipeline_collapse",
    "sample_cells",
    "sample_genes",
    "set_cellbench_bpparam",
    "set_cellbench_cache_path",
    "set_cellbench_threads",
    "split_step",
    "strip_timing",
    "time_methods",
    "unpack_timing"
  ],
  "_datasets": [
    {
      "name": "sample_sce_data",
      "title": "This is data for testing functions in CellBench.",
      "object": "sample_sce_data",
      "file": "sample_sce_data.rda",
      "class": [
        "SingleCellExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "CellBench-package",
      "title": "A framework for benchmarking combinations of methods in multi-stage pipelines",
      "topics": [
        "CellBench-package",
        "CellBench"
      ]
    },
    {
      "page": "any_task_errors",
      "title": "Check if any tasks produced errors",
      "topics": [
        "any_task_errors",
        "any_task_errors.benchmark_tbl"
      ]
    },
    {
      "page": "apply_methods",
      "title": "Apply methods",
      "topics": [
        "apply_methods",
        "apply_methods.benchmark_tbl",
        "apply_methods.list",
        "apply_methods.tbl_df",
        "apply_metrics",
        "begin_benchmark"
      ]
    },
    {
      "page": "arrow_sep",
      "title": "Unicode arrow separators",
      "topics": [
        "arrow_sep"
      ]
    },
    {
      "page": "as_pipeline_list",
      "title": "convert benchmark_tbl to list",
      "topics": [
        "as_pipeline_list"
      ]
    },
    {
      "page": "cache_method",
      "title": "Create a cached function for CellBench",
      "topics": [
        "cache_method"
      ]
    },
    {
      "page": "cellbench_case_study",
      "title": "Open vignetted containing a case study using CellBench",
      "topics": [
        "cellbench_case_study"
      ]
    },
    {
      "page": "cellbench_file",
      "title": "Get path to CellBench packaged data",
      "topics": [
        "cellbench_file"
      ]
    },
    {
      "page": "clear_cached_datasets",
      "title": "Clear cached datasets",
      "topics": [
        "clear_cached_datasets"
      ]
    },
    {
      "page": "clear_cellbench_cache",
      "title": "Clear CellBench Cache",
      "topics": [
        "clear_cellbench_cache"
      ]
    },
    {
      "page": "collapse_pipeline",
      "title": "Collapse benchmark_tbl into a two column summary",
      "topics": [
        "collapse_pipeline",
        "pipeline_collapse"
      ]
    },
    {
      "page": "data_list",
      "title": "Constructor for a data list",
      "topics": [
        "data_list"
      ]
    },
    {
      "page": "filter_zero_genes",
      "title": "Filter out zero count genes",
      "topics": [
        "filter_zero_genes"
      ]
    },
    {
      "page": "fn_arg_seq",
      "title": "Create a list of functions with arguments varying over a sequence",
      "topics": [
        "fn_arg_seq"
      ]
    },
    {
      "page": "fn_list",
      "title": "Constructor for a function list",
      "topics": [
        "fn_list"
      ]
    },
    {
      "page": "is.task_error",
      "title": "Check for task errors",
      "topics": [
        "is.task_error"
      ]
    },
    {
      "page": "keep_high_count_cells",
      "title": "Filter down to the highest count cells",
      "topics": [
        "keep_high_count_cells"
      ]
    },
    {
      "page": "keep_high_count_genes",
      "title": "Filter down to the highest count genes",
      "topics": [
        "keep_high_count_genes"
      ]
    },
    {
      "page": "keep_high_var_genes",
      "title": "Filter down to the most variable genes",
      "topics": [
        "keep_high_var_genes"
      ]
    },
    {
      "page": "load_all_data",
      "title": "Load CellBench Data",
      "topics": [
        "load_all_data",
        "load_cell_mix_data",
        "load_mrna_mix_data",
        "load_sc_data"
      ]
    },
    {
      "page": "mhead",
      "title": "Get head of 2 dimensional object as a square block",
      "topics": [
        "mhead"
      ]
    },
    {
      "page": "sample_cells",
      "title": "Sample cells from a SingleCellExperiment",
      "topics": [
        "sample_cells"
      ]
    },
    {
      "page": "sample_genes",
      "title": "Sample genes from a SingleCellExperiment",
      "topics": [
        "sample_genes"
      ]
    },
    {
      "page": "sample_sce_data",
      "title": "This is data for testing functions in CellBench.",
      "topics": [
        "sample_sce_data"
      ]
    },
    {
      "page": "set_cellbench_bpparam",
      "title": "Set BiocParallel parameter used CellBench",
      "topics": [
        "set_cellbench_bpparam"
      ]
    },
    {
      "page": "set_cellbench_cache_path",
      "title": "Set CellBench cache path",
      "topics": [
        "set_cellbench_cache_path"
      ]
    },
    {
      "page": "set_cellbench_threads",
      "title": "Set number of threads used by CellBench",
      "topics": [
        "set_cellbench_threads"
      ]
    },
    {
      "page": "split_step",
      "title": "Split combined pipeline step",
      "topics": [
        "split_step"
      ]
    },
    {
      "page": "time_methods",
      "title": "Time methods",
      "topics": [
        "time_methods",
        "time_methods.benchmark_timing_tbl",
        "time_methods.list"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CellBench/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "assertthat",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "httr2",
    "IRanges",
    "lambda.r",
    "lattice",
    "lifecycle",
    "lubridate",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "openssl",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rappdirs",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "utf8",
    "vctrs",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "DataManipulation.Rmd",
      "filename": "DataManipulation.html",
      "title": "Benchmark Data Manipulation",
      "author": "Shian Su",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Benchmark Tibble",
        "Basics",
        "Operations On Benchmark Tibbles",
        "Operations On list-columns",
        "Unnesting with Lists of data.frames",
        "Manipulating Functions",
        "Basics of Functional Programming",
        "Partial Application",
        "Sequence of Partial Applications",
        "Memoisation",
        "Further Reading"
      ],
      "created": "2018-11-07 06:28:49",
      "modified": "2022-10-21 03:47:25",
      "commits": 9
    },
    {
      "source": "Introduction.Rmd",
      "filename": "Introduction.html",
      "title": "Introduction to CellBench",
      "author": "Shian Su",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Quick start",
        "Downloading benchmark data",
        "Key objects and concepts",
        "Function piping",
        "Mapping or list-apply",
        "List of datasets",
        "List of functions",
        "Benchmark tibble and list-columns",
        "Applying methods",
        "Advanced usage",
        "Multithreading",
        "Function return caching",
        "Constructing functions with parameter range",
        "Summary"
      ],
      "created": "2018-10-17 11:20:53",
      "modified": "2023-02-22 06:21:14",
      "commits": 25
    },
    {
      "source": "TidyversePatterns.Rmd",
      "filename": "TidyversePatterns.html",
      "title": "Tidyverse Patterns",
      "author": "Shian Su",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Functional Programming with purrr",
        "Methods as Function Objects",
        "Function Composition",
        "Mapping Over Lists",
        "Table Manipulation with dplyr",
        "Operations on the Benchmark tibble",
        "Calculating multiple columns of metrics",
        "Plotting with ggplot2",
        "Basic Plotting",
        "Facetting"
      ],
      "created": "2019-03-08 01:35:05",
      "modified": "2022-10-21 03:47:25",
      "commits": 3
    },
    {
      "source": "Timing.Rmd",
      "filename": "Timing.html",
      "title": "Timing methods in CellBench",
      "author": "Shian Su",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Timing methods",
        "Summary"
      ],
      "created": "2019-01-22 05:46:05",
      "modified": "2019-02-06 06:26:39",
      "commits": 2
    },
    {
      "source": "WritingWrappers.Rmd",
      "filename": "WritingWrappers.html",
      "title": "Writing Wrappers",
      "author": "Shian Su",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Wrapper Guidelines",
        "Practical Examples",
        "Simple Wrapper",
        "Final remarks"
      ],
      "created": "2019-03-29 02:36:17",
      "modified": "2019-08-09 07:50:09",
      "commits": 3
    }
  ],
  "_score": 8.977357729545302,
  "_indexed": true,
  "_nocasepkg": "cellbench",
  "_universes": [
    "bioc",
    "shians"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-29T08:30:52.000Z",
      "distro": "noble",
      "commit": "1afd28752fe95dd818da1b0e61de197e5617dff5",
      "fileid": "ba1180926b42100acbfe8db7a0cac35415ccee192e85a517fdb1a5e0e272e198",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626603621"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-29T08:31:09.000Z",
      "distro": "noble",
      "commit": "1afd28752fe95dd818da1b0e61de197e5617dff5",
      "fileid": "7800135326b4708329ceb4d37767a8237cba998f423277060b2392bd24bee5db",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626603621"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-29T10:09:49.000Z",
      "commit": "1afd28752fe95dd818da1b0e61de197e5617dff5",
      "fileid": "9dcfd266b70d21ff4cea06b6f206a7e01a11aa4715209a4b29465f8acdc47adc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626603621"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-29T10:09:56.000Z",
      "commit": "1afd28752fe95dd818da1b0e61de197e5617dff5",
      "fileid": "5f4a4d58c389e784d2fef250b82791fab457a5aaa9d472385bff2e28a0042b80",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626603621"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.29.0",
      "date": "2026-05-29T08:30:41.000Z",
      "commit": "1afd28752fe95dd818da1b0e61de197e5617dff5",
      "fileid": "d40233b3f27fe4a881c2322fecd30d1070867856a9147613cace6135befc37f2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626603621"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-29T08:29:33.000Z",
      "commit": "1afd28752fe95dd818da1b0e61de197e5617dff5",
      "fileid": "23fca36abaa33a5060729af356a39f2fabc4ff2149cc9559e93a2a45c07efade",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626603621"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-29T08:29:36.000Z",
      "commit": "1afd28752fe95dd818da1b0e61de197e5617dff5",
      "fileid": "b49dd47d7033ee16c91a6ef1f7bc8a9aa8a5bc394efb5b3e5b413c9c5d690c76",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626603621"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-29T08:29:44.000Z",
      "commit": "1afd28752fe95dd818da1b0e61de197e5617dff5",
      "fileid": "3d86b821b3df9f9a978c02d93779a58513600de35fb18c9d1e0bca26e8a0f50d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626603621"
    }
  ]
}