{ "_id": "6af31a6ef58eaab799207f32", "Package": "EmbedSOM", "Version": "2.2.1", "Title": "Fast Embedding Guided by Self-Organizing Map", "Authors@R": "c(person(\"Mirek\", \"Kratochvil\",\nrole = c(\"aut\", \"cre\"),\nemail = \"exa.exa@gmail.com\"),\nperson(\"Sofie\", \"Van Gassen\",\nrole = \"cph\",\nemail = \"sofie.vangassen@ugent.be\"),\nperson(\"Britt\", \"Callebaut\",\nrole = \"cph\",\nemail = \"britt.callebaut@ugent.be\"),\nperson(\"Yvan\", \"Saeys\",\nrole = \"cph\",\nemail = \"yvan.saeys@ugent.be\"),\nperson(\"Ron\", \"Wehrens\",\nrole = \"cph\",\nemail = \"ron.wehrens@gmail.com\"))", "Description": "Provides a smooth mapping of multidimensional points into\nlow-dimensional space defined by a self-organizing map.\nDesigned to work with 'FlowSOM' and flow-cytometry use-cases.\nSee Kratochvil et al. (2019)\n.", "License": "GPL (>= 3)", "URL": "https://github.com/exaexa/EmbedSOM", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev libpng-dev libxml2-dev libssl-dev\npython3", "Repository": "https://exaexa.r-universe.dev", "Date/Publication": "2026-03-08 21:27:35 UTC", "RemoteUrl": "https://github.com/exaexa/embedsom", "RemoteRef": "HEAD", "RemoteSha": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-11-10 12:50:49 UTC", "User": "root" }, "Author": "Mirek Kratochvil [aut, cre],\nSofie Van Gassen [cph],\nBritt Callebaut [cph],\nYvan Saeys [cph],\nRon Wehrens [cph]", "Maintainer": "Mirek Kratochvil ", "_user": "exaexa", "_type": "src", "_file": "EmbedSOM_2.2.1.tar.gz", "_fileid": "https://r2.ropensci.org/526244dfc4264598911cfb673a79811c4204a080928c77d909e46b16044647cd", "_filesize": 6011655, "_sha256": "526244dfc4264598911cfb673a79811c4204a080928c77d909e46b16044647cd", "_expires": "2027-02-18T13:21:48.000Z", "_created": "2026-11-10T12:50:49.000Z", "_published": "2026-11-10T13:21:50.125Z", "_upstream": "https://github.com/exaexa/embedsom", "_status": "success", "_maintainer": { "name": "Mirek Kratochvil", "email": "exa.exa@gmail.com", "login": "exaexa", "mastodon": "@exa@mastodon.online", "description": "I used a computer once.", "uuid": 271543 }, "_jobs": [ { "job": 129840419216, "time": 131, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "13765144103" }, { "job": 129840419615, "time": 149, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13765764485" }, { "job": 129840419273, "time": 119, "config": "linux-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13765104115" }, { "job": 129840419398, "time": 149, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13765784620" }, { "job": 129840419114, "time": 127, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13766399448" }, { "job": 129840419133, "time": 268, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13767742222" }, { "job": 129840419057, "time": 168, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13768175457" }, { "job": 129840419092, "time": 231, "config": "macos-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13767573817" }, { "job": 129838253671, "time": 265, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13765223928" }, { "job": 129840419028, "time": 114, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13765574518" }, { "job": 129840419337, "time": 256, "config": "windows-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "13766039074" }, { "job": 129840419186, "time": 148, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13766375197" }, { "job": 129840419099, "time": 100, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13765114105" }, { "job": 129840419103, "time": 231, "config": "windows-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13766193678" }, { "job": 129840419197, "time": 148, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13766325309" } ], "_buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848", "_commit": { "id": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "author": "Mirek Kratochvil ", "committer": "Mirek Kratochvil ", "message": "regen roxygen\n", "time": 1773005255 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "Rtsne", "role": "Imports" }, { "package": "umap", "role": "Imports" }, { "package": "uwot", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "exaexa", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-10", "n": 4 } ], "_tags": [ { "name": "v2.2.1", "date": "2026-03-08" } ], "_topics": [ "cytometry", "som", "visualization", "cpp" ], "_stars": 26, "_contributors": [ { "user": "exaexa", "count": 148, "uuid": 271543 }, { "user": "samgg", "count": 2, "uuid": 3333348 } ], "_userbio": { "uuid": 271543, "type": "user", "name": "Mirek Kratochvil", "followers": 134, "description": "I used a computer once." }, "_downloads": { "count": 565, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/EmbedSOM" }, "_mentions": 4, "_devurl": "https://github.com/exaexa/embedsom", "_searchresults": 8, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/EmbedSOM.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/exaexa/embedsom", "_realowner": "exaexa", "_cranurl": true, "_releases": [ { "version": "1.9", "date": "2019-08-19" }, { "version": "1.9.1", "date": "2019-08-19" }, { "version": "2.1.1", "date": "2020-02-12" }, { "version": "2.1.2", "date": "2022-07-05" }, { "version": "2.2", "date": "2025-01-31" }, { "version": "2.2.1", "date": "2026-03-10" } ], "_exports": [ "ClusterPalette", "EmbedSOM", "ExprColors", "ExpressionGradient", "ExpressionPalette", "GQTSOM", "GraphCoords", "Initialize_PCA", "kMeansMap", "kNNCoords", "MapDataToCodes", "MSTCoords", "NormalizeColor", "PlotData", "PlotDefault", "PlotEmbed", "PlotGG", "RandomMap", "SOM", "tSNECoords", "UMAPCoords", "UMatrixCoords", "uwotCoords" ], "_help": [ { "page": "ClusterPalette", "title": "An acceptable cluster color palette", "topics": [ "ClusterPalette" ] }, { "page": "EmbedSOM", "title": "Process the cells with SOM into a nice embedding", "topics": [ "EmbedSOM" ] }, { "page": "ExprColors", "title": "Generate colors for multi-color marker expression labeling in a single plot", "topics": [ "ExprColors" ] }, { "page": "ExpressionGradient", "title": "The ggplot2 scale gradient from ExpressionPalette.", "topics": [ "ExpressionGradient" ] }, { "page": "ExpressionPalette", "title": "Marker expression palette generator based off ColorBrewer's RdYlBu, only better for plotting of half-transparent cells", "topics": [ "ExpressionPalette" ] }, { "page": "GQTSOM", "title": "Train a Growing Quadtree Self-Organizing Map", "topics": [ "GQTSOM" ] }, { "page": "GraphCoords", "title": "Add Kamada-Kawai-generated embedding coordinates to the map", "topics": [ "GraphCoords" ] }, { "page": "Initialize_PCA", "title": "Create a grid from first 2 PCA components", "topics": [ "Initialize_PCA" ] }, { "page": "kMeansMap", "title": "Create a map from k-Means clusters", "topics": [ "kMeansMap" ] }, { "page": "kNNCoords", "title": "Add KNN-topology-based embedding coordinates to the map", "topics": [ "kNNCoords" ] }, { "page": "MapDataToCodes", "title": "Assign nearest node to each datapoint", "topics": [ "MapDataToCodes" ] }, { "page": "MSTCoords", "title": "Add MST-style embedding coordinates to the map", "topics": [ "MSTCoords" ] }, { "page": "NormalizeColor", "title": "Helper for computing colors for embedding plots", "topics": [ "NormalizeColor" ] }, { "page": "PlotData", "title": "Export a data frame for plotting with marker intensities and density.", "topics": [ "PlotData" ] }, { "page": "PlotDefault", "title": "Default plot", "topics": [ "PlotDefault" ] }, { "page": "PlotEmbed", "title": "Helper function for plotting the embedding", "topics": [ "PlotEmbed" ] }, { "page": "PlotGG", "title": "Wrap PlotData result in ggplot object.", "topics": [ "PlotGG" ] }, { "page": "PlotId", "title": "Identity on whatever", "topics": [ "PlotId" ] }, { "page": "RandomMap", "title": "Create a map by randomly selecting points", "topics": [ "RandomMap" ] }, { "page": "SOM", "title": "Build a self-organizing map", "topics": [ "SOM" ] }, { "page": "tSNECoords", "title": "Add tSNE-based coordinates to a map", "topics": [ "tSNECoords" ] }, { "page": "UMAPCoords", "title": "Add UMAP-based coordinates to a map", "topics": [ "UMAPCoords" ] }, { "page": "UMatrixCoords", "title": "Add U-Matrix-optimized embedding coordinates to the map", "topics": [ "UMatrixCoords" ] }, { "page": "uwotCoords", "title": "Add UMAP-based coordinates to a map, using the 'uwot' package", "topics": [ "uwotCoords" ] } ], "_readme": "https://github.com/exaexa/embedsom/raw/HEAD/README.md", "_rundeps": [ "askpass", "BH", "cli", "cpp11", "dqrng", "farver", "FNN", "ggplot2", "glue", "gtable", "here", "igraph", "irlba", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "openssl", "pkgconfig", "png", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppEigen", "RcppProgress", "RcppTOML", "reticulate", "rlang", "rprojroot", "RSpectra", "Rtsne", "S7", "scales", "sitmo", "sys", "umap", "uwot", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "UsingEmbedSOM.Rmd", "filename": "UsingEmbedSOM.html", "title": "EmbedSOM basic embedding", "author": "Mirek Kratochvil", "engine": "knitr::rmarkdown", "headings": [ "Basic embedding with EmbedSOM", "Dataset", "Getting the SOM ready", "Embedding", "Plotting the data" ], "created": "2019-12-10 09:21:46", "modified": "2020-01-18 10:23:26", "commits": 2 } ], "_score": 5.7160033436347994, "_indexed": true, "_nocasepkg": "embedsom", "_universes": [ "exaexa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.2.1", "date": "2026-11-10T12:53:08.000Z", "distro": "resolute", "arch": "aarch64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/f0ea1fba880ac5ae200b82a7370e37964f7f5f11a067ec532097ae0ec3e21521", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.7.0", "os": "linux", "version": "2.2.1", "date": "2026-11-10T12:53:23.000Z", "distro": "resolute", "arch": "x86_64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/168b1ab95060981bd0a9b4d6336a6358f09546a4b90c9cda38d1b7fc6c73a002", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.6.2", "os": "linux", "version": "2.2.1", "date": "2026-11-10T12:53:02.000Z", "distro": "resolute", "arch": "aarch64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/1d7fb1a350981501d2346a0c22c9759d51b7614a66559c4a31862bfa747a5e8f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.6.2", "os": "linux", "version": "2.2.1", "date": "2026-11-10T12:53:25.000Z", "distro": "resolute", "arch": "x86_64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/f2fc6751cafe1619a068a1ae7a29c1bb93f0a665c8ea265bde6adb7734106296", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.5.3", "os": "mac", "version": "2.2.1", "date": "2026-11-10T13:18:41.000Z", "arch": "aarch64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/4edfe46d9f31ede018358e2ab23cc1dce35abef3ef78099c2a3fc57de7e33e3d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.5.3", "os": "mac", "version": "2.2.1", "date": "2026-11-10T13:11:39.000Z", "arch": "x86_64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/a1a88c8ebde935c9c33b6905984460956d646c5e492c76ef65ffdf8fc9fd639b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.6.2", "os": "mac", "version": "2.2.1", "date": "2026-11-10T13:19:15.000Z", "arch": "aarch64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/1fc3045f055bdb13c5baa70ba8b53c8a3756be2f562f923e565122160bea583b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.6.2", "os": "mac", "version": "2.2.1", "date": "2026-11-10T13:20:03.000Z", "arch": "x86_64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/15c8831ed05104bf8ab6078d4710352ff1095c0ca49dbca3721cd6da92f65524", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.6.0", "os": "wasm", "version": "2.2.1", "date": "2026-11-10T12:53:11.000Z", "arch": "emscripten", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/970eb0a68b1267b06e84e35f1dfdc72a2e30c3b3bbca7b83afc93e08c30c41cf", "status": "success", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.7.0", "os": "win", "version": "2.2.1", "date": "2026-11-10T12:55:02.000Z", "arch": "aarch64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/4eb36494b8332c0dc59f62968bbdce31d751622c8526ba72851d3fe62eb24d2e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.7.0", "os": "win", "version": "2.2.1", "date": "2026-11-10T12:52:31.000Z", "arch": "x86_64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/04e1c934ccb1acdf42f1c5c16fa1095b849e1ff12aa9704681148f8cd4f6b425", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.5.3", "os": "win", "version": "2.2.1", "date": "2026-11-10T12:52:28.000Z", "arch": "x86_64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/fca7c169e7610372a8e2135320ff31d1d1771da1e8bd15701401cc48be8b6a05", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.6.2", "os": "win", "version": "2.2.1", "date": "2026-11-10T12:54:39.000Z", "arch": "aarch64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/ebd3ddecc015c62a598b542f5c9b1d705b067b2827af73bf36aded0ec8674192", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" }, { "r": "4.6.2", "os": "win", "version": "2.2.1", "date": "2026-11-10T12:52:30.000Z", "arch": "x86_64", "commit": "734f57824ae7dabf75f9d79ae3db23bd694e556a", "fileid": "https://r2.ropensci.org/00829595a46767fa608cf36f60c844897f5b36034c87419882b8faaa0238b38d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/exaexa/actions/runs/42818628848" } ] }