{ "_id": "6a4f53ea21b18e1548500b97", "Package": "CytoSimplex", "Type": "Package", "Title": "Simplex Visualization of Cell Fate Similarity in Single-Cell\nData", "Version": "0.2.0", "Date": "2025-04-22", "Authors@R": "c(\nperson(given = 'Yichen', family = 'Wang', email = 'wayichen@umich.edu',\nrole = c('aut', 'cre'), comment = c(ORCID = \"0000-0003-4347-5199\")),\nperson(given = 'Jialin', family = 'Liu', email = 'alanliu@umich.edu',\nrole = c('aut'), comment = c(ORCID = \"0000-0002-9984-7695\")),\nperson(given = 'Joshua', family = 'Welch', email = 'welchjd@umich.edu',\nrole = c('cph'))\n)", "Maintainer": "Yichen Wang ", "Description": "Create simplex plots to visualize the similarity between\nsingle-cells and selected clusters in a 1-/2-/3-simplex space.\nVelocity information can be added as an additional layer. See\nLiu J, Wang Y et al (2023) \nfor more details.", "URL": "https://welch-lab.github.io/CytoSimplex/,\nhttps://github.com/welch-lab/CytoSimplex", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "biocViews": "", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev", "Repository": "https://welch-lab.r-universe.dev", "Date/Publication": "2025-04-23 14:10:26 UTC", "RemoteUrl": "https://github.com/welch-lab/CytoSimplex", "RemoteRef": "HEAD", "RemoteSha": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-09 07:46:56 UTC", "User": "root" }, "Author": "Yichen Wang [aut, cre] (ORCID: ),\nJialin Liu [aut] (ORCID: ),\nJoshua Welch [cph]", "_user": "welch-lab", "_type": "src", "_file": "CytoSimplex_0.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/742c05a267b536d27dbfd1cea372a35a238ac9a3b97c500a63d929b653e03045", "_filesize": 2815754, "_sha256": "742c05a267b536d27dbfd1cea372a35a238ac9a3b97c500a63d929b653e03045", "_expires": "2026-10-17T07:55:20.000Z", "_created": "2026-07-09T07:46:56.000Z", "_published": "2026-07-09T07:55:22.405Z", "_jobs": [ { "job": 86066589202, "time": 255, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8192271825" }, { "job": 86066589187, "time": 275, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8192277130" }, { "job": 86066589205, "time": 244, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8192268255" }, { "job": 86066589210, "time": 273, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8192276567" }, { "job": 86066589197, "time": 207, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8192254319" }, { "job": 86066589209, "time": 364, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8192307456" }, { "job": 86066589218, "time": 247, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8192267881" }, { "job": 86066589178, "time": 419, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8192325799" }, { "job": 86065565899, "time": 362, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8192183933" }, { "job": 86066589636, "time": 192, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8192249325" }, { "job": 86066589229, "time": 207, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8192254805" }, { "job": 86066589216, "time": 210, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8192255948" }, { "job": 86066589167, "time": 254, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8192270430" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158", "_status": "success", "_upstream": "https://github.com/welch-lab/CytoSimplex", "_commit": { "id": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "author": "Yichen Wang ", "committer": "Yichen Wang ", "message": "Reorganize to reduce installed size\n", "time": 1745417426 }, "_maintainer": { "name": "Yichen Wang", "email": "wayichen@umich.edu", "login": "mvfki", "linkedin": "in/wangych-12044417a", "twitter": "@wyc_mvfki", "description": "Bioinformatician Intermediate @welch-lab , DCMB, UofM // Previously @campbio // MS in Bioinformatics, BU // BS in Life Science, ShanghaiTech University", "uuid": 28736557, "orcid": "0000-0003-4347-5199" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "stats", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "grDevices", "role": "Depends" }, { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "cli", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "plot3D", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "hdf5r", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "magick", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" }, { "package": "SeuratObject", "role": "Suggests" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "welch-lab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 6, "_contributors": [ { "user": "mvfki", "count": 74, "uuid": 28736557 }, { "user": "skpalan", "count": 1, "uuid": 49622175 }, { "user": "ttriche", "count": 1, "uuid": 4386 } ], "_userbio": { "uuid": 45493916, "type": "organization", "name": "welch-lab", "followers": 48 }, "_downloads": { "count": 577, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CytoSimplex" }, "_devurl": "https://github.com/welch-lab/cytosimplex", "_pkgdown": "https://welch-lab.github.io/CytoSimplex/", "_searchresults": 5, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/CytoSimplex.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/welch-lab/cytosimplex", "_realowner": "welch-lab", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2023-12-13" }, { "version": "0.1.1", "date": "2023-12-15" }, { "version": "0.2.0", "date": "2025-04-23" } ], "_exports": [ "colNormalize", "plotBinary", "plotQuaternary", "plotTernary", "readH5ADObsNames", "readH5ADObsVar", "readH5ADUnsSpMat", "readVelocytoLoom", "selectTopFeatures", "writeQuaternaryGIF" ], "_datasets": [ { "name": "rnaCluster", "title": "Major cell type annotation of the example mouse bone marrow data", "object": "rnaCluster", "class": [ "factor" ], "fields": [], "table": false, "tojson": true }, { "name": "rnaRaw", "title": "Mouse bone marrow scRNAseq example data", "object": "rnaRaw", "class": [ "dgCMatrix" ], "fields": [], "table": false, "tojson": false }, { "name": "rnaVelo", "title": "Velocity graph of the example mouse bone marrow data", "object": "rnaVelo", "class": [ "dgCMatrix" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "colNormalize", "title": "Normalize each column of the input matrix by the column sum", "topics": [ "colNormalize", "colNormalize.default", "colNormalize.dgCMatrix", "colNormalize.Seurat", "colNormalize.SingleCellExperiment" ] }, { "page": "plotBinary", "title": "Create binary plots", "topics": [ "plotBinary", "plotBinary.default", "plotBinary.Seurat", "plotBinary.simMat", "plotBinary.SingleCellExperiment" ] }, { "page": "plotQuaternary", "title": "Create quaternary simplex plots", "concept": [ "plotQuaternary" ], "topics": [ "plotQuaternary", "plotQuaternary.default" ] }, { "page": "plotQuaternary.Seurat", "title": "Craete quaternary simplex plot with Seurat object", "concept": [ "plotQuaternary" ], "topics": [ "plotQuaternary.Seurat" ] }, { "page": "plotQuaternary.simMat", "title": "Create quaternary simplex plot with pre-calculated similarity matrix", "topics": [ "plotQuaternary.simMat" ] }, { "page": "plotQuaternary.SingleCellExperiment", "title": "Create quaternary simplex plot with SingleCellExperiment object", "concept": [ "plotQuaternary" ], "topics": [ "plotQuaternary.SingleCellExperiment" ] }, { "page": "plotTernary", "title": "Create ternary simplex plots", "concept": [ "plotTernary" ], "topics": [ "plotTernary", "plotTernary.default" ] }, { "page": "plotTernary.Seurat", "title": "Create ternary simplex plot with Seurat objects", "concept": [ "plotTernary" ], "topics": [ "plotTernary.Seurat" ] }, { "page": "plotTernary.simMat", "title": "Create quaternary simplex plot with pre-calculated similarity matrix", "topics": [ "plotTernary.simMat" ] }, { "page": "plotTernary.SingleCellExperiment", "title": "Create ternary simplex plot with SingleCellExperiment objects", "concept": [ "plotTernary" ], "topics": [ "plotTernary.SingleCellExperiment" ] }, { "page": "print-quatPlot", "title": "Show plist object produced with plot3D package", "topics": [ "print.quatPlot" ] }, { "page": "readH5ADObsNames", "title": "Extract `adata.obs_names` from an H5AD file", "concept": [ "H5AD-reader" ], "topics": [ "readH5ADObsNames" ] }, { "page": "readH5ADObsVar", "title": "Extract a variable from adata.obs stored in an H5AD file", "concept": [ "H5AD-reader" ], "topics": [ "readH5ADObsVar" ] }, { "page": "readH5ADUnsSpMat", "title": "Extract a sparse matrix from adata.uns stored in an H5AD file", "concept": [ "H5AD-reader" ], "topics": [ "readH5ADUnsSpMat" ] }, { "page": "readVelocytoLoom", "title": "Extract the raw counts from a LOOM file", "concept": [ "H5AD-reader" ], "topics": [ "readVelocytoLoom" ] }, { "page": "rnaCluster", "title": "Major cell type annotation of the example mouse bone marrow data", "topics": [ "rnaCluster" ] }, { "page": "rnaRaw", "title": "Mouse bone marrow scRNAseq example data", "topics": [ "rnaRaw" ] }, { "page": "rnaVelo", "title": "Velocity graph of the example mouse bone marrow data", "topics": [ "rnaVelo" ] }, { "page": "selectTopFeatures", "title": "Pick top differentially presented features for similarity calculation", "topics": [ "selectTopFeatures", "selectTopFeatures.default", "selectTopFeatures.Seurat", "selectTopFeatures.SingleCellExperiment" ] }, { "page": "writeQuaternaryGIF", "title": "Create GIF image for dynamic rotating view of 3D quaternary simplex plot", "topics": [ "writeQuaternaryGIF" ] } ], "_pkglogo": "https://github.com/welch-lab/CytoSimplex/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/welch-lab/CytoSimplex/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bslib", "cachem", "cli", "cpp11", "crosstalk", "curl", "data.table", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "magrittr", "Matrix", "memoise", "mime", "misc3d", "openssl", "otel", "pillar", "pkgconfig", "plot3D", "plotly", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "yaml" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "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": "CytoSimplex.Rmd", "filename": "CytoSimplex.html", "title": "Simplex Visualization of Cell Fate Similarity in Single-Cell Data", "author": "Yichen Wang, Jialin Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Example Data", "Select top features (optional but recommended)", "Generating ternary plots", "Interactive ternary plot", "Adding velocity information to ternary plot", "Exploration with each cluster", "Create quaternary simplex plot" ], "created": "2023-09-26 18:59:54", "modified": "2025-04-23 14:10:26", "commits": 10 } ], "_score": 4.778151250383644, "_indexed": true, "_nocasepkg": "cytosimplex", "_universes": [ "welch-lab", "mvfki" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-07-09T07:50:34.000Z", "distro": "resolute", "arch": "aarch64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/2178e9a714f19e67d8d0107909e1a77d827923fc8e2dae316b33c37a555056dc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-07-09T07:50:29.000Z", "distro": "resolute", "arch": "x86_64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/bb4baf70f7524b9fdbdcb3b4dc73b46cdc6bcc13be8fdb53f49ec2ccfc2bbcf4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.6.1", "os": "linux", "version": "0.2.0", "date": "2026-07-09T07:50:25.000Z", "distro": "resolute", "arch": "aarch64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/8b2bea959fc4f66bebba8d429dead5bd875301a735912ae2a8c91d098ec663d6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.6.1", "os": "linux", "version": "0.2.0", "date": "2026-07-09T07:50:26.000Z", "distro": "resolute", "arch": "x86_64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/a174df84d762e8a245b5f85060ec6c5a8d9fda57498cdab1992623dc87cdca8f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.5.3", "os": "mac", "version": "0.2.0", "date": "2026-07-09T07:49:26.000Z", "arch": "aarch64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/e2751c7f7965147d11781d65aa219f7fb6355dada5caffe23b5e6b76e4f195a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.5.3", "os": "mac", "version": "0.2.0", "date": "2026-07-09T07:50:52.000Z", "arch": "x86_64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/ea1b17e37ebc98e6e45d18d96059c5eade3fda63d452fa2f99c39b2e20ae8625", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.6.1", "os": "mac", "version": "0.2.0", "date": "2026-07-09T07:49:39.000Z", "arch": "aarch64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/a9e1c13c295d0d408c2c368df6769defed2e17fb6b0f73d3986c8799b6f07848", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.6.1", "os": "mac", "version": "0.2.0", "date": "2026-07-09T07:51:23.000Z", "arch": "x86_64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/8421d83bba0843981207d6f6e353263e8eb658514fd4ba160d11c9e5ef317399", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.0", "date": "2026-07-09T07:50:40.000Z", "arch": "emscripten", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/c0a088e0a09775b9d9f0f34af089cef77f7c92bc657e32b3d81a42b68f9a83cd", "status": "success", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.7.0", "os": "win", "version": "0.2.0", "date": "2026-07-09T07:49:02.000Z", "arch": "x86_64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/8ba6f0f1cc10d89e2391dfe931a70d235689bddd723691ab03bcca4d947a9bd7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.5.3", "os": "win", "version": "0.2.0", "date": "2026-07-09T07:49:05.000Z", "arch": "x86_64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/2da9fa968d143ddf449cbd5fea92d6a7c185086df4d80fd7e7058eeb89da3dce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" }, { "r": "4.6.1", "os": "win", "version": "0.2.0", "date": "2026-07-09T07:49:28.000Z", "arch": "x86_64", "commit": "d8a252f08ac8067c1426ec85f600c94a9d99c8a0", "fileid": "https://r2.ropensci.org/1942b2a5e0074960ad3fa48ec226ed1e2ff7162157de5f6b66ef199c6d7f77be", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/welch-lab/actions/runs/29002297158" } ] }