{ "_id": "6a154836acfb0bcc41d58053", "Package": "phateR", "Title": "PHATE - Potential of Heat-Diffusion for Affinity-Based\nTransition Embedding", "Version": "1.0.7", "Authors@R": "c(person(\"Krishnan\", \"Srinivasan\", email = \"krishnan.srinivasan@yale.edu\", role = c(\"aut\")),\nperson(given = 'Scott', family = 'Gigante', email = 'scott.gigante@yale.edu', role = 'cre', comment = c(ORCID = '0000-0002-4544-2764')))", "Description": "PHATE is a tool for visualizing high dimensional\nsingle-cell data with natural progressions or trajectories.\nPHATE uses a novel conceptual framework for learning and\nvisualizing the manifold inherent to biological systems in\nwhich smooth transitions mark the progressions of cells from\none state to another. To see how PHATE can be applied to\nsingle-cell RNA-seq datasets from hematopoietic stem cells,\nhuman embryonic stem cells, and bone marrow samples, check out\nour publication in Nature Biotechnology at\n.", "License": "GPL-2 | file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 07:09:56 UTC", "User": "root" }, "Author": "Krishnan Srinivasan [aut], Scott Gigante [cre]\n()", "Maintainer": "Scott Gigante ", "Config/pak/sysreqs": "libpng-dev python3", "Repository": "https://scottgigante.r-universe.dev", "Date/Publication": "2021-02-12 09:00:02 UTC", "RemoteUrl": "https://github.com/cran/phateR", "RemoteRef": "HEAD", "RemoteSha": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "MD5sum": "fdf8e0d54804498f0a344ae6816e7eed", "_user": "scottgigante", "_type": "src", "_file": "phateR_1.0.7.tar.gz", "_fileid": "18394184e2554b474859e8a7cd7fcf26802d2c90b175c49c90174e21b24b9959", "_filesize": 3859115, "_sha256": "18394184e2554b474859e8a7cd7fcf26802d2c90b175c49c90174e21b24b9959", "_created": "2026-05-26T07:09:56.000Z", "_published": "2026-05-26T07:13:58.747Z", "_distro": "noble", "_jobs": [ { "job": 77824723989, "time": 151, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7210959706" }, { "job": 77824723937, "time": 159, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7210961267" }, { "job": 77824723988, "time": 203, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7210964556" }, { "job": 77824724003, "time": 168, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7210955306" }, { "job": 77824261621, "time": 206, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7210915896" }, { "job": 77824723958, "time": 105, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7210947017" }, { "job": 77824723948, "time": 167, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7210964126" }, { "job": 77824723932, "time": 166, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7210963776" }, { "job": 77824723944, "time": 166, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7210964323" } ], "_buildurl": "https://github.com/r-universe/scottgigante/actions/runs/26437688695", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/phateR", "_commit": { "id": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "author": "Scott Gigante ", "committer": "cran-robot ", "message": "version 1.0.7\n", "time": 1613120402 }, "_maintainer": { "name": "Scott Gigante", "email": "scott.gigante@yale.edu", "login": "scottgigante", "description": "Head of Engineering & Founding Engineer, Sightline Climate", "uuid": 8499679, "orcid": "0000-0002-4544-2764" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3", "role": "Depends" }, { "package": "Matrix", "version": ">= 1.2-0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "reticulate", "version": ">= 1.8", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "memoise", "role": "Imports" }, { "package": "gridGraphics", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "scottgigante", "count": 9, "uuid": 8499679 } ], "_userbio": { "uuid": 8499679, "type": "user", "name": "Scott Gigante", "description": "Head of Engineering & Founding Engineer, Sightline Climate" }, "_downloads": { "count": 438, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phateR" }, "_mentions": 4, "_searchresults": 370, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/phateR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "scottgigante", "_cranurl": false, "_releases": [ { "version": "0.2.6", "date": "2018-05-27" }, { "version": "0.2.7", "date": "2018-06-01" }, { "version": "0.2.8", "date": "2018-07-03" }, { "version": "0.2.9", "date": "2018-09-11" }, { "version": "0.4.0", "date": "2019-04-13" }, { "version": "0.4.1", "date": "2019-04-26" }, { "version": "1.0.0", "date": "2019-12-05" }, { "version": "1.0.4", "date": "2020-05-22" }, { "version": "1.0.7", "date": "2021-02-12" } ], "_exports": [ "check_pyphate_version", "cluster_phate", "install.phate", "library.size.normalize", "phate" ], "_datasets": [ { "name": "tree.data", "title": "Fake branching data for examples", "object": "tree.data", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "tree.data.small", "title": "Fake branching data for running examples fast", "object": "tree.data.small", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "as.data.frame", "title": "Convert a PHATE object to a data.frame", "topics": [ "as.data.frame.phate" ] }, { "page": "as.matrix", "title": "Convert a PHATE object to a matrix", "topics": [ "as.matrix.phate" ] }, { "page": "check_pyphate_version", "title": "Check that the current PHATE version in Python is up to date.", "topics": [ "check_pyphate_version" ] }, { "page": "cluster_phate", "title": "KMeans on the PHATE potential Clustering on the PHATE operator as introduced in Moon et al. This is similar to spectral clustering.", "topics": [ "cluster_phate" ] }, { "page": "ggplot", "title": "Convert a PHATE object to a data.frame for ggplot", "topics": [ "ggplot.phate" ] }, { "page": "install.phate", "title": "Install PHATE Python Package", "topics": [ "install.phate" ] }, { "page": "library.size.normalize", "title": "Performs L1 normalization on input data such that the sum of expression values for each cell sums to 1, then returns normalized matrix to the metric space using median UMI count per cell effectively scaling all cells as if they were sampled evenly.", "topics": [ "library.size.normalize" ] }, { "page": "phate", "title": "Run PHATE on an input data matrix", "topics": [ "phate" ] }, { "page": "plot", "title": "Plot a PHATE object in base R", "topics": [ "plot.phate" ] }, { "page": "print", "title": "Print a PHATE object", "topics": [ "print.phate" ] }, { "page": "summary", "title": "Summarize a PHATE object", "topics": [ "summary.phate" ] }, { "page": "tree.data", "title": "Fake branching data for examples", "topics": [ "tree.data" ] }, { "page": "tree.data.small", "title": "Fake branching data for running examples fast", "topics": [ "tree.data.small" ] } ], "_readme": "https://github.com/cran/phateR/raw/HEAD/README.md", "_rundeps": [ "cachem", "cli", "cpp11", "farver", "fastmap", "ggplot2", "glue", "gtable", "here", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "Matrix", "memoise", "png", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppTOML", "reticulate", "rlang", "rprojroot", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_score": 3.8692317197309762, "_indexed": true, "_nocasepkg": "phater", "_universes": [ "scottgigante" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.7", "date": "2026-05-26T07:12:09.000Z", "distro": "noble", "commit": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "fileid": "cb6eda4298c964b9f86a7533dbaeda50cdbe8636ddaf19597af52ce01c87c3fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/scottgigante/actions/runs/26437688695" }, { "r": "4.6.0", "os": "linux", "version": "1.0.7", "date": "2026-05-26T07:12:14.000Z", "distro": "noble", "commit": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "fileid": "f1961290127caf6307743d3a8a00826a6feaa11d096e6c1a120d2aabfa39b697", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/scottgigante/actions/runs/26437688695" }, { "r": "4.5.3", "os": "mac", "version": "1.0.7", "date": "2026-05-26T07:12:29.000Z", "commit": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "fileid": "fd02e548b209ac77ca5d50fe9af0b3bb59a951865937ddf00fff05e7f282a80b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/scottgigante/actions/runs/26437688695" }, { "r": "4.6.0", "os": "mac", "version": "1.0.7", "date": "2026-05-26T07:11:58.000Z", "commit": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "fileid": "f095f6ea9bccac177afc8fe52572765938bcba05cf32d46437d7d6155a9edec0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/scottgigante/actions/runs/26437688695" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.7", "date": "2026-05-26T07:12:03.000Z", "commit": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "fileid": "be5fdf631b9046bb92f20bcf5b1f20458a188d7aec8bd610f4a7e7dae3a6d3ca", "status": "success", "buildurl": "https://github.com/r-universe/scottgigante/actions/runs/26437688695" }, { "r": "4.7.0", "os": "win", "version": "1.0.7", "date": "2026-05-26T07:11:16.000Z", "commit": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "fileid": "4a261ebb779890f22a973fc9471384997a96b1a8fc4c54a5209b3f51be6c1bf6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/scottgigante/actions/runs/26437688695" }, { "r": "4.5.3", "os": "win", "version": "1.0.7", "date": "2026-05-26T07:11:18.000Z", "commit": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "fileid": "612ec37ec907fb9b2898201eccd44ab94c653d3ea59720b10c4d038a0562a609", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/scottgigante/actions/runs/26437688695" }, { "r": "4.6.0", "os": "win", "version": "1.0.7", "date": "2026-05-26T07:11:08.000Z", "commit": "e0cd10e1ed560ff20c66b0d9cc4089264fde74a4", "fileid": "5c73d47da6131e37e18e5ae482c45075bf4cd0a95c480fce549ab391be079298", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/scottgigante/actions/runs/26437688695" } ] }