{ "_id": "6a13f0bfacfb0bcc41d30687", "Package": "SuperCellCyto", "Title": "SuperCell For Cytometry Data", "Version": "1.3.0", "Authors@R": "c(\nperson(\"Givanna\", \"Putri\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-7399-8014\"), email = \"givanna.h@gmail.com\"),\nperson(\"George\", \"Howitt\", role = \"aut\"),\nperson(\"Felix\", \"Marsh-Wakefield\", role = \"aut\"),\nperson(\"Thomas\", \"Ashhurst\", role = \"aut\"),\nperson(\"Belinda\", \"Phipson\", role = \"aut\"))", "Description": "SuperCellCyto provides the ability to summarise cytometry\ndata into supercells by merging together cells that are similar\nin their marker expressions using the SuperCell package.", "biocViews": "CellBiology, FlowCytometry, Software, SingleCell", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "URL": "https://phipsonlab.github.io/SuperCellCyto/", "BugReports": "https://github.com/phipsonlab/SuperCellCyto/issues", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 libx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:05:31 UTC", "RemoteUrl": "https://github.com/bioc/SuperCellCyto", "RemoteRef": "HEAD", "RemoteSha": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 06:38:45 UTC", "User": "root" }, "Author": "Givanna Putri [aut, cre] (ORCID:\n),\nGeorge Howitt [aut],\nFelix Marsh-Wakefield [aut],\nThomas Ashhurst [aut],\nBelinda Phipson [aut]", "Maintainer": "Givanna Putri ", "MD5sum": "6edd8c9b82d178bd1405827ab21fbcbf", "_user": "bioc", "_type": "src", "_file": "SuperCellCyto_1.3.0.tar.gz", "_fileid": "ef3d81fa5ab85f3bc4c96cabc0c9a92f82f4ed1c9e335661c945d1d92c2a6870", "_filesize": 3540721, "_sha256": "ef3d81fa5ab85f3bc4c96cabc0c9a92f82f4ed1c9e335661c945d1d92c2a6870", "_created": "2026-05-25T06:38:45.000Z", "_published": "2026-05-25T06:48:31.199Z", "_jobs": [ { "job": 77668065944, "time": 204, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7193042269" }, { "job": 77668065946, "time": 483, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7193104488" }, { "job": 77668065955, "time": 553, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7193119250" }, { "job": 77668065951, "time": 308, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7193065736" }, { "job": 77668065961, "time": 332, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7193071251" }, { "job": 77667375590, "time": 383, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7192993225" }, { "job": 77668065943, "time": 190, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7193039301" }, { "job": 77668065962, "time": 385, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7193083084" }, { "job": 77668065948, "time": 377, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7193081436" }, { "job": 77668065947, "time": 388, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7193084287" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 2 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26386903621", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/SuperCellCyto", "_commit": { "id": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381531 }, "_maintainer": { "name": "Givanna Putri", "email": "givanna.h@gmail.com", "login": "ghar1821", "description": "", "uuid": 5366317, "orcid": "0000-0002-7399-8014" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "SuperCell", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "flowCore", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "usethis", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BiocSingular", "role": "Suggests" }, { "package": "bluster", "role": "Suggests" }, { "package": "scater", "role": "Suggests" }, { "package": "scran", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "magick", "role": "Suggests" }, { "package": "qs2", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-33", "n": 2 }, { "week": "2025-34", "n": 1 }, { "week": "2025-39", "n": 2 }, { "week": "2025-42", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.3.0", "bioc": "3.24" }, { "branch": "release", "version": "1.2.0", "bioc": "3.23" } ], "_topics": [ "cellbiology", "flowcytometry", "software", "singlecell", "bioinformatics", "computational-biology", "cytometry" ], "_stars": 13, "_contributors": [ { "user": "ghar1821", "count": 87, "uuid": 5366317 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 214, "source": "https://www.bioconductor.org/packages/stats/bioc/SuperCellCyto" }, "_devurl": "https://github.com/phipsonlab/supercellcyto", "_pkgdown": "https://phipsonlab.github.io/SuperCellCyto/", "_searchresults": 22, "_rbuild": "4.6.0", "_assets": [ "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", "extra/SuperCellCyto.html", "manual.pdf" ], "_homeurl": "https://github.com/phipsonlab/supercellcyto", "_realowner": "bioc", "_cranurl": false, "_exports": [ "recomputeSupercells", "runSuperCellCyto", "simCytoData" ], "_help": [ { "page": "recomputeSupercells", "title": "Recompute supercells", "topics": [ "recomputeSupercells" ] }, { "page": "runSuperCellCyto", "title": "Run SuperCellCyto on Cytometry Data", "topics": [ "runSuperCellCyto" ] }, { "page": "simCytoData", "title": "Simulate cytometry data", "topics": [ "simCytoData" ] } ], "_readme": "https://github.com/bioc/SuperCellCyto/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "base64enc", "BH", "BiocParallel", "bit", "bit64", "boot", "broom", "bslib", "cachem", "checkmate", "cli", "clipr", "cluster", "codetools", "colorspace", "corpcor", "cpp11", "crayon", "data.table", "dbscan", "digest", "dplyr", "entropy", "evaluate", "farver", "fastmap", "fontawesome", "forcats", "foreach", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "gdata", "generics", "ggplot2", "glmnet", "glue", "gridExtra", "gtable", "gtools", "haven", "here", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "igraph", "irlba", "isoband", "iterators", "jomo", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "lattice", "lifecycle", "lme4", "magrittr", "MASS", "Matrix", "matrixStats", "memoise", "mice", "mime", "minqa", "mitml", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "ordinal", "pan", "patchwork", "pillar", "pkgconfig", "plotfunctions", "plyr", "png", "prettyunits", "progress", "proxy", "purrr", "R6", "RANN", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "RcppTOML", "Rdpack", "readr", "reformulas", "reticulate", "rlang", "rmarkdown", "rpart", "rprojroot", "RSpectra", "rstudioapi", "Rtsne", "S7", "sass", "scales", "shape", "snow", "stringi", "stringr", "SuperCell", "survival", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "ucminf", "umap", "utf8", "vctrs", "viridisLite", "vroom", "weights", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "SuperCellCyto.Rmd", "filename": "SuperCellCyto.html", "title": "How to create supercells", "author": "Givanna Putri", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Preparing your dataset", "Creating supercells", "Supercell object", "Supercell expression matrix", "SuperCellId", "Supercell cell map", "Running runSuperCellCyto in parallel", "Controlling supercells granularity", "Adjusting gamma value after one run of runSuperCellCyto", "Specifying different gamma value for different samples", "Mixing cells from different samples in a supercell", "I have more cells than RAM in my computer", "Session information" ], "created": "2025-09-22 05:52:57", "modified": "2025-09-22 05:52:57", "commits": 1 }, { "source": "how_to_prepare_data.Rmd", "filename": "how_to_prepare_data.html", "title": "How to Prepare Data for SuperCellCyto", "author": "Givanna Putri", "engine": "knitr::rmarkdown", "headings": [ "Performing Quality Control", "Preparing FCS/CSV files for SuperCellCyto", "Cell ID column", "Sample column", "Preparing CSV files", "Preparing FCS files", "Data Transformation", "Session information" ], "created": "2024-01-19 05:22:55", "modified": "2025-09-22 05:52:57", "commits": 6 }, { "source": "interoperability_with_seurat.Rmd", "filename": "interoperability_with_seurat.html", "title": "Interoperability with Seurat", "author": "Givanna Putri", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Preparing Seurat object", "Run SuperCellCyto", "Analyse Supercells as Seurat object", "Transfer information from supercells to single-cell Seurat object", "Session information" ], "created": "2024-01-24 03:39:17", "modified": "2025-09-22 05:52:57", "commits": 5 }, { "source": "interoperability_with_sce.Rmd", "filename": "interoperability_with_sce.html", "title": "Interoperability with SingleCellExperiment", "author": "Givanna Putri", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Preparing SCE object", "Run SuperCellCyto", "Analyse Supercells as SCE object", "Transfer information from supercells SCE object to single cell SCE object", "Session information" ], "created": "2024-01-24 03:39:17", "modified": "2025-10-14 02:39:25", "commits": 7 }, { "source": "using_supercellcyto_for_stratified_summarising.Rmd", "filename": "using_supercellcyto_for_stratified_summarising.html", "title": "Using SuperCellCyto for Stratified Summarising", "author": "Givanna Putri", "engine": "knitr::rmarkdown", "headings": [ "Session information" ], "created": "2024-01-22 22:43:54", "modified": "2025-09-22 05:52:57", "commits": 4 } ], "_score": 6.632457292184725, "_indexed": true, "_nocasepkg": "supercellcyto", "_universes": [ "bioc", "ghar1821", "phipsonlab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-05-25T06:43:12.000Z", "distro": "noble", "commit": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "fileid": "c878c034b3211543c3a0323b9081621c94babeea65db64aab2d6448f23823b40", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26386903621" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-05-25T06:45:10.000Z", "distro": "noble", "commit": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "fileid": "7bd56cadce13ce882093ed77daef0c006485cedb224ac6603a250302715540ce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26386903621" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-05-25T06:40:50.000Z", "commit": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "fileid": "753ea57619efedaa7bdd06d4dcca5f0118be5178eec8e6acc60cacf82f161785", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26386903621" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-05-25T06:40:48.000Z", "commit": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "fileid": "3a27e4b5c62620aa134c28fd1006d863e2dd0eda0d2445cebcdd824497ca618e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26386903621" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-05-25T06:42:12.000Z", "commit": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "fileid": "44466a341e202fc563121f264d44efe40fbb0e2be631760e647bd87f66de48b9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26386903621" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-05-25T06:40:48.000Z", "commit": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "fileid": "20957b009bd95f5ee072d238a7808887ab202a4622dc8a67cfa1aab1f6107b22", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26386903621" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-05-25T06:40:55.000Z", "commit": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "fileid": "87668ffcc3a9a93b3a8b1905c0725b06e3c11e3906489df4a70848dc620ec73d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26386903621" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-05-25T06:41:06.000Z", "commit": "a36270636d3c0b9d37122f94e2e3c8fb5f6ae891", "fileid": "24a6b326ffbe52d262a997f5e42d51c578c3b268b286bc2ddb31373d440dba01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26386903621" } ] }