{ "_id": "6a103493acfb0bcc41c99365", "Package": "CytOpT", "Type": "Package", "Title": "Optimal Transport for Gating Transfer in Cytometry Data with\nDomain Adaptation", "Version": "0.9.8", "Date": "2025-03-31", "Authors@R": "c(person(\"Boris\", \"Hejblum\", role = c(\"aut\", \"cre\"), email = \"boris.hejblum@u-bordeaux.fr\"),\nperson(\"Paul\", \"Freulon\", role = c(\"aut\"), email = \"paul.freulon@math.u-bordeaux.fr\"),\nperson(\"Kalidou\", \"Ba\", role = c(\"aut\", \"trl\")))", "Maintainer": "Boris Hejblum ", "SystemRequirements": "Python (>= 3.7)", "Description": "Supervised learning from a source distribution (with known\nsegmentation into cell sub-populations) to fit a target\ndistribution with unknown segmentation. It relies regularized\noptimal transport to directly estimate the different cell\npopulation proportions from a biological sample characterized\nwith flow cytometry measurements. It is based on the\nregularized Wasserstein metric to compare cytometry\nmeasurements from different samples, thus accounting for\npossible mis-alignment of a given cell population across sample\n(due to technical variability from the technology of\nmeasurements). Supervised learning technique based on the\nWasserstein metric that is used to estimate an optimal\nre-weighting of class proportions in a mixture model Details\nare presented in Freulon P, Bigot J and Hejblum BP (2023)\n.", "License": "GPL (>= 2)", "URL": "https://sistm.github.io/CytOpT-R/,\nhttps://github.com/sistm/CytOpT-R/", "LazyData": "true", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Language": "en-US", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev python3", "Repository": "https://sistm.r-universe.dev", "Date/Publication": "2025-03-31 22:03:28 UTC", "RemoteUrl": "https://github.com/sistm/cytopt-r", "RemoteRef": "HEAD", "RemoteSha": "3981460b3acd799ce196d454999c9c7057f69206", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-12 07:44:53 UTC", "User": "root" }, "Author": "Boris Hejblum [aut, cre],\nPaul Freulon [aut],\nKalidou Ba [aut, trl]", "MD5sum": "374cbc2fc30cd826a27fbe90a2128e92", "_user": "sistm", "_type": "src", "_file": "CytOpT_0.9.8.tar.gz", "_fileid": "240d218fee06ae3caad8344433562483db5d4cdd25a94fca2f0549c079c07824", "_filesize": 2013406, "_sha256": "240d218fee06ae3caad8344433562483db5d4cdd25a94fca2f0549c079c07824", "_created": "2026-05-12T07:44:53.000Z", "_published": "2026-05-22T10:48:51.711Z", "_distro": "noble", "_jobs": [ { "job": 77364630694, "time": 137, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6938497908" }, { "job": 77364630564, "time": 207, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6938517775" }, { "job": 77364630742, "time": 192, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6938501450" }, { "job": 77364630444, "time": 211, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6938510617" }, { "job": 77364630179, "time": 200, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6938457058" }, { "job": 77364629960, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7158697960" }, { "job": 77364630786, "time": 107, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6938489297" }, { "job": 77364630821, "time": 110, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6938490120" }, { "job": 77364630496, "time": 99, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6938487238" } ], "_buildurl": "https://github.com/r-universe/sistm/actions/runs/25720637610", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/sistm/cytopt-r", "_commit": { "id": "3981460b3acd799ce196d454999c9c7057f69206", "author": "borishejblum ", "committer": "borishejblum ", "message": "also limiting threads during tests\n", "time": 1743458608 }, "_maintainer": { "name": "Boris Hejblum", "email": "boris.hejblum@u-bordeaux.fr", "login": "borishejblum", "uuid": 5277851 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "ggplot2", "version": ">= 3.0.0", "role": "Imports" }, { "package": "MetBrewer", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "reticulate", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "sistm", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "borishejblum", "count": 118, "uuid": 5277851 }, { "user": "kalidouba", "count": 46, "uuid": 64191365 } ], "_userbio": { "uuid": 38222472, "type": "organization", "name": "SISTM", "description": "research team from Inserm BPH U1219 & Inria BSO" }, "_downloads": { "count": 260, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CytOpT" }, "_devurl": "https://github.com/sistm/cytopt-r", "_pkgdown": "https://sistm.github.io/CytOpT-R/", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/CytOpT.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/sistm/cytopt-r", "_realowner": "sistm", "_cranurl": true, "_releases": [ { "version": "0.9.2", "date": "2022-02-07" }, { "version": "0.9.4", "date": "2022-02-09" }, { "version": "0.9.6", "date": "2025-03-26" }, { "version": "0.9.7", "date": "2025-03-30" }, { "version": "0.9.8", "date": "2025-04-01" } ], "_exports": [ "barplot_prop", "Bland_Altman", "CytOpT", "cytopt_desasc_r", "cytopt_minmax_r", "KL_plot", "Label_Prop_sto_r" ], "_datasets": [ { "name": "HIPC_Stanford_1228_1A", "title": "HIPC_Stanford data", "object": "HIPC_Stanford", "class": [ "data.frame" ], "fields": [ "CCR7", "CD4", "CD45RA", "CD3", "HLADR", "CD38", "CD8" ], "rows": 31342, "table": true, "tojson": true }, { "name": "HIPC_Stanford_1228_1A_labels", "title": "HIPC_Stanford data", "object": "HIPC_Stanford", "class": [ "factor" ], "fields": [], "table": false, "tojson": true }, { "name": "HIPC_Stanford_1369_1A", "title": "HIPC_Stanford data", "object": "HIPC_Stanford", "class": [ "data.frame" ], "fields": [ "CCR7", "CD4", "CD45RA", "CD3", "HLADR", "CD38", "CD8" ], "rows": 33992, "table": true, "tojson": true }, { "name": "HIPC_Stanford_1369_1A_labels", "title": "HIPC_Stanford data", "object": "HIPC_Stanford", "class": [ "factor" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "barplot_prop", "title": "Function to display a bland plot in order to visually assess the agreement between CytOpt estimation of the class proportions and the estimate of the class proportions provided through manual gating.", "topics": [ "barplot_prop" ] }, { "page": "Bland_Altman", "title": "Bland & Altman plot", "topics": [ "Bland_Altman" ] }, { "page": "CytOpT", "title": "Function to estimate the type cell proportions in an unclassified cytometry data set denoted X_s by using the classification Lab_source from an other cytometry data set X_s. With this function the computation of the estimate of the class proportions is done with a descent ascent or minmax or two algorithms.", "topics": [ "CytOpT" ] }, { "page": "cytopt_desasc_r", "title": "Function to estimate the type cell proportions in an unclassified cytometry data set denoted X_s by using the classification Lab_source from an other cytometry data set X_s. With this function the computation of the estimate of the class proportions is done with a descent ascent algorithm.", "topics": [ "cytopt_desasc_r" ] }, { "page": "cytopt_minmax_r", "title": "Function to estimate the type cell proportions in an unclassified cytometry data set denoted X_s by using the classification Lab_source from an other cytometry data set X_s. With this function an additional regularization parameter on the class proportions enables a faster computation of the estimator.", "topics": [ "cytopt_minmax_r" ] }, { "page": "HIPC_Stanford", "title": "HIPC_Stanford data", "topics": [ "HIPC_Stanford", "HIPC_Stanford_1228_1A", "HIPC_Stanford_1228_1A_labels", "HIPC_Stanford_1369_1A", "HIPC_Stanford_1369_1A_labels" ] }, { "page": "KL_plot", "title": "Kullback-Leibler divergence plot", "topics": [ "KL_plot" ] }, { "page": "Label_Prop_sto_r", "title": "Computes a classification on the target data", "topics": [ "Label_Prop_sto_r" ] }, { "page": "plot.CytOpt", "title": "CytOpt plot", "topics": [ "plot.CytOpt" ] }, { "page": "print.CytOpt", "title": "CytOpt print", "topics": [ "print.CytOpt" ] }, { "page": "print.summary.CytOpt", "title": "CytOpt print summary", "topics": [ "print.summary.CytOpt" ] }, { "page": "summary.CytOpt", "title": "CytOpt summary", "topics": [ "summary.CytOpt" ] } ], "_pkglogo": "https://github.com/sistm/cytopt-r/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/sistm/cytopt-r/raw/HEAD/README.md", "_rundeps": [ "brio", "callr", "cli", "cpp11", "crayon", "desc", "diffobj", "evaluate", "farver", "fs", "ggplot2", "glue", "gtable", "here", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "MetBrewer", "patchwork", "pkgbuild", "pkgload", "plyr", "png", "praise", "processx", "ps", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppTOML", "reshape2", "reticulate", "rlang", "rprojroot", "S7", "scales", "stringi", "stringr", "testthat", "vctrs", "viridisLite", "waldo", "withr" ], "_vignettes": [ { "source": "CytOpt_HIPC.Rmd", "filename": "CytOpt_HIPC.html", "title": "User guide for executing CytOpT on HIPC data", "author": "Paul Freulon, Jérémie Bigot, Kalidou BA, Boris Hejblum", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Analysis of HIPC data", "Data load", "Computation of the benchmark class proportions for target data", "CytOpT", "Optimization", "Results", "Performance evaluation" ], "created": "2022-01-24 15:45:32", "modified": "2025-03-31 21:28:45", "commits": 21 } ], "_score": 3.6989700043360187, "_indexed": true, "_nocasepkg": "cytopt", "_universes": [ "sistm", "borishejblum" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.9.8", "date": "2026-05-12T07:46:59.000Z", "distro": "noble", "commit": "3981460b3acd799ce196d454999c9c7057f69206", "fileid": "1a0c53f95d77fee41d2a49569015a1d103bf9f1c479dbb3e7b846f120c06cc8a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/25720637610" }, { "r": "4.6.0", "os": "linux", "version": "0.9.8", "date": "2026-05-12T07:47:59.000Z", "distro": "noble", "commit": "3981460b3acd799ce196d454999c9c7057f69206", "fileid": "912808fcf891e0841d7dc132058cc544a1a8240f0a34ac6c2f72d6db0be49cee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/25720637610" }, { "r": "4.5.3", "os": "mac", "version": "0.9.8", "date": "2026-05-12T07:47:13.000Z", "commit": "3981460b3acd799ce196d454999c9c7057f69206", "fileid": "91e637aa65d610416c1af7f5b5ea6e6333ba13836992cdf5204bb563d943d67d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/25720637610" }, { "r": "4.6.0", "os": "mac", "version": "0.9.8", "date": "2026-05-12T07:47:35.000Z", "commit": "3981460b3acd799ce196d454999c9c7057f69206", "fileid": "4b509c4a96385069f3c9813810ef407d2c571fe50591fdf6244a4e69b9a909f4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/25720637610" }, { "r": "4.7.0", "os": "win", "version": "0.9.8", "date": "2026-05-12T07:46:21.000Z", "commit": "3981460b3acd799ce196d454999c9c7057f69206", "fileid": "d3ec5130863e0f62d19e90324eb9f5eae61b31b4d3910bff483f5182b973a9db", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/25720637610" }, { "r": "4.5.3", "os": "win", "version": "0.9.8", "date": "2026-05-12T07:46:25.000Z", "commit": "3981460b3acd799ce196d454999c9c7057f69206", "fileid": "67f829607afdd054a5badbe1f11b154443bc5c5cfe3ed60bcf70f27bcbc13af6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/25720637610" }, { "r": "4.6.0", "os": "win", "version": "0.9.8", "date": "2026-05-12T07:46:17.000Z", "commit": "3981460b3acd799ce196d454999c9c7057f69206", "fileid": "28e014663cd5e36e2e91c1688ef032c5b4fdc07137267cd5ea5fdc72e9f0ffeb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/25720637610" }, { "r": "4.6.0", "os": "wasm", "version": "0.9.8", "date": "2026-05-22T10:48:30.000Z", "commit": "3981460b3acd799ce196d454999c9c7057f69206", "fileid": "e38d210238fffc4dc774d7e413fa0622bee378e5ea18ed2e5912b0844377540c", "status": "success", "buildurl": "https://github.com/r-universe/sistm/actions/runs/25720637610" } ] }