{ "_id": "6a494a7ff6c47c4419498b3e", "Package": "TrajectoryGeometry", "Title": "This Package Discovers Directionality in Time and Pseudo-times\nSeries of Gene Expression Patterns", "Version": "1.21.0", "Authors@R": "person(given = \"Anna\",\nfamily = \"Laddach\",\nrole = c(\"aut\", \"cre\"),\nemail = \"anna.laddach@crick.ac.uk\",\ncomment = c(ORCID = \"0000-0001-5552-6534\"))\nperson(given = \"Michael\",\nfamily = \"Shapiro\",\nrole = c(\"aut\", \"cre\"),\nemail = \"michael.shapiro@crick.ac.uk\",\ncomment = c(ORCID = \"0000-0002-2769-9320\"))", "Description": "Given a time series or pseudo-times series of gene\nexpression data, we might wish to know: Do the changes in gene\nexpression in these data exhibit directionality? Are there\nturning points in this directionality. Do different subsets of\nthe data move in different directions? This package uses\nspherical geometry to probe these sorts of questions. In\nparticular, if we are looking at (say) the first n dimensions\nof the PCA of gene expression, directionality can be detected\nas the clustering of points on the (n-1)-dimensional sphere.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "biocViews": "BiologicalQuestion, StatisticalMethod, GeneExpression,\nSingleCell", "Config/pak/sysreqs": "cmake libfreetype6-dev libglu1-mesa-dev make\ntexlive libpng-dev libuv1-dev libgl1-mesa-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:54:58 UTC", "RemoteUrl": "https://github.com/bioc/TrajectoryGeometry", "RemoteRef": "HEAD", "RemoteSha": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 16:16:55 UTC", "User": "root" }, "Author": "Michael Shapiro [aut, cre] (ORCID:\n)", "Maintainer": "Michael Shapiro ", "_user": "bioc", "_type": "src", "_file": "TrajectoryGeometry_1.21.0.tar.gz", "_fileid": "https://r2.ropensci.org/30b9baeef0d6566a8b89debaa61c40eb61b161af54ac689d43110421ea3930eb", "_filesize": 2626318, "_sha256": "30b9baeef0d6566a8b89debaa61c40eb61b161af54ac689d43110421ea3930eb", "_expires": "2026-10-12T18:01:32.000Z", "_created": "2026-07-03T16:16:55.000Z", "_published": "2026-07-04T18:01:35.507Z", "_bioccheck": { "error": 0, "warning": 1, "note": 11 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28671903850", "_status": "success", "_upstream": "https://github.com/bioc/TrajectoryGeometry", "_commit": { "id": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380898 }, "_maintainer": { "name": "Michael Shapiro", "email": "michael.shapiro@crick.ac.uk", "orcid": "0000-0002-2769-9320" }, "_distro": "resolute", "_jobs": [ { "job": 85154480116, "time": 186, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8071072862" }, { "job": 85154480257, "time": 216, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8071081070" }, { "job": 85154480234, "time": 220, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8071081960" }, { "job": 85154480333, "time": 140, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8071060690" }, { "job": 85154480264, "time": 137, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8071059948" }, { "job": 85154480106, "time": 332, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8071023007" }, { "job": 85154480192, "time": 144, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8071061975" }, { "job": 85154480107, "time": 122, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8071056235" }, { "job": 85154480212, "time": 118, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8071055298" }, { "job": 85154480318, "time": 106, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8071052163" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "pracma", "role": "Imports" }, { "package": "rgl", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "dplyr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "biologicalquestion", "statisticalmethod", "geneexpression", "singlecell" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 8, "_rbuild": "4.6.1", "_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/TrajectoryGeometry.html", "LICENSE", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "analyseBranchPoint", "analyseSingleCellTrajectory", "circleOnTheUnitSphere", "distanceBetweenTrajectories", "findSphereClusterCenter", "findSphericalDistance", "generateRandomPaths", "generateRandomUnitVector", "getDistanceDataForPaths", "getSphericalData", "getStepLengths", "orthonormalBasis", "pathProgression", "pathToSphericalData", "plotPathProjectionCenterAndCircle", "projectPathToSphere", "samplePath", "testPathForDirectionality", "visualiseBranchPointStats", "visualiseTrajectoryStats" ], "_datasets": [ { "name": "chol_answers", "title": "chol_answers", "object": "chol_answers", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "chol_attributes", "title": "chol_attributes", "object": "chol_attributes", "class": [ "matrix", "array" ], "fields": [ "PC_1", "PC_2", "PC_3", "PC_4", "PC_5", "PC_6", "PC_7", "PC_8", "PC_9", "PC_10" ], "rows": 229, "table": true, "tojson": true }, { "name": "chol_branch_point_results", "title": "chol_branch_point_results", "object": "chol_branch_point_results", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "chol_pseudo_time", "title": "chol_pseudo_time", "object": "chol_pseudo_time", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "chol_pseudo_time_normalised", "title": "chol_pseudo_time_normalised", "object": "chol_pseudo_time_normalised", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "crooked_path", "title": "Crooked path", "object": "crooked_path", "class": [ "matrix", "array" ], "fields": [], "rows": 14, "table": true, "tojson": true }, { "name": "crooked_path_center", "title": "Crooked path center", "object": "crooked_path_center", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "crooked_path_projection", "title": "Crooked path projection", "object": "crooked_path_projection", "class": [ "matrix", "array" ], "fields": [], "rows": 8, "table": true, "tojson": true }, { "name": "crooked_path_radius", "title": "Crooked path radius", "object": "crooked_path_radius", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "hep_answers", "title": "hep_answers", "object": "hep_answers", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "hep_attributes", "title": "hep_attributes", "object": "hep_attributes", "class": [ "matrix", "array" ], "fields": [ "PC_1", "PC_2", "PC_3", "PC_4", "PC_5", "PC_6", "PC_7", "PC_8", "PC_9", "PC_10" ], "rows": 360, "table": true, "tojson": true }, { "name": "hep_pseudo_time", "title": "hep_pseudo_time", "object": "hep_pseudo_time", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "hep_pseudo_time_normalised", "title": "hep_pseudo_time_normalised", "object": "hep_pseudo_time_normalised", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "oscillation", "title": "Oscillation", "object": "oscillation", "class": [ "matrix", "array" ], "fields": [], "rows": 20, "table": true, "tojson": true }, { "name": "single_cell_matrix", "title": "single_cell_matrix", "object": "single_cell_matrix", "class": [ "matrix", "array" ], "fields": [ "PC_1", "PC_2", "PC_3", "PC_4", "PC_5", "PC_6", "PC_7", "PC_8", "PC_9", "PC_10" ], "rows": 447, "table": true, "tojson": true }, { "name": "straight_path", "title": "Straight path", "object": "straight_path", "class": [ "matrix", "array" ], "fields": [], "rows": 14, "table": true, "tojson": true }, { "name": "straight_path_center", "title": "Straight path center", "object": "straight_path_center", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "straight_path_projection", "title": "Straight path projection", "object": "straight_path_projection", "class": [ "matrix", "array" ], "fields": [], "rows": 13, "table": true, "tojson": true }, { "name": "straight_path_radius", "title": "Straight path radius", "object": "straight_path_radius", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "analyseBranchPoint", "title": "Analyse branch point.", "topics": [ "analyseBranchPoint" ] }, { "page": "analyseSingleCellTrajectory", "title": "Analyse a single cell trajectory.", "topics": [ "analyseSingleCellTrajectory" ] }, { "page": "chol_answers", "title": "chol_answers", "topics": [ "chol_answers" ] }, { "page": "chol_attributes", "title": "chol_attributes", "topics": [ "chol_attributes" ] }, { "page": "chol_branch_point_results", "title": "chol_branch_point_results", "topics": [ "chol_branch_point_results" ] }, { "page": "chol_pseudo_time", "title": "chol_pseudo_time", "topics": [ "chol_pseudo_time" ] }, { "page": "chol_pseudo_time_normalised", "title": "chol_pseudo_time_normalised", "topics": [ "chol_pseudo_time_normalised" ] }, { "page": "circleOnTheUnitSphere", "title": "Circle on the unit sphere", "topics": [ "circleOnTheUnitSphere" ] }, { "page": "crooked_path", "title": "Crooked path", "topics": [ "crooked_path" ] }, { "page": "crooked_path_center", "title": "Crooked path center", "topics": [ "crooked_path_center" ] }, { "page": "crooked_path_projection", "title": "Crooked path projection", "topics": [ "crooked_path_projection" ] }, { "page": "crooked_path_radius", "title": "Crooked path radius", "topics": [ "crooked_path_radius" ] }, { "page": "distanceBetweenTrajectories", "title": "Get distances between trajectories.", "topics": [ "distanceBetweenTrajectories" ] }, { "page": "findSphereClusterCenter", "title": "Find a center for points on the unit sphere", "topics": [ "findSphereClusterCenter" ] }, { "page": "findSphericalDistance", "title": "Find the spherical distance from a given point to a set of points.", "topics": [ "findSphericalDistance" ] }, { "page": "generateRandomPaths", "title": "Produce random paths modeled on a given path", "topics": [ "generateRandomPaths" ] }, { "page": "generateRandomUnitVector", "title": "Generate random unit vector.", "topics": [ "generateRandomUnitVector" ] }, { "page": "getDistanceDataForPaths", "title": "Produce distance statistics for random paths", "topics": [ "getDistanceDataForPaths" ] }, { "page": "getSphericalData", "title": "This is a simplified wrapper for pathToSphericalData", "topics": [ "getSphericalData" ] }, { "page": "getStepLengths", "title": "Find the step lengths:", "topics": [ "getStepLengths" ] }, { "page": "hep_answers", "title": "hep_answers", "topics": [ "hep_answers" ] }, { "page": "hep_attributes", "title": "hep_attributes", "topics": [ "hep_attributes" ] }, { "page": "hep_pseudo_time", "title": "hep_pseudo_time", "topics": [ "hep_pseudo_time" ] }, { "page": "hep_pseudo_time_normalised", "title": "hep_pseudo_time_normalised", "topics": [ "hep_pseudo_time_normalised" ] }, { "page": "orthonormalBasis", "title": "Find an orthonormal basis in dimension 3", "topics": [ "orthonormalBasis" ] }, { "page": "oscillation", "title": "Oscillation", "topics": [ "oscillation" ] }, { "page": "pathProgression", "title": "Measure a path's progression", "topics": [ "pathProgression" ] }, { "page": "pathToSphericalData", "title": "Find the spherical data for a given path", "topics": [ "pathToSphericalData" ] }, { "page": "plotPathProjectionCenterAndCircle", "title": "Plot a path, its projection, its center and its circle", "topics": [ "plotPathProjectionCenterAndCircle" ] }, { "page": "projectPathToSphere", "title": "Project a path onto the unit sphere", "topics": [ "projectPathToSphere" ] }, { "page": "samplePath", "title": "Sample a path from single cell data", "topics": [ "samplePath" ] }, { "page": "single_cell_matrix", "title": "single_cell_matrix", "topics": [ "single_cell_matrix" ] }, { "page": "straight_path", "title": "Straight path", "topics": [ "straight_path" ] }, { "page": "straight_path_center", "title": "Straight path center", "topics": [ "straight_path_center" ] }, { "page": "straight_path_projection", "title": "Straight path projection", "topics": [ "straight_path_projection" ] }, { "page": "straight_path_radius", "title": "Straight path radius", "topics": [ "straight_path_radius" ] }, { "page": "testPathForDirectionality", "title": "Test a path for directionality", "topics": [ "testPathForDirectionality" ] }, { "page": "visualiseBranchPointStats", "title": "Visualise Branch Point Stats", "topics": [ "visualiseBranchPointStats" ] }, { "page": "visualiseTrajectoryStats", "title": "Visualise Trajectory Stats", "topics": [ "visualiseTrajectoryStats" ] } ], "_readme": "https://github.com/bioc/TrajectoryGeometry/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bslib", "cachem", "cli", "cpp11", "digest", "evaluate", "farver", "fastmap", "fontawesome", "fs", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lifecycle", "magrittr", "memoise", "mime", "pracma", "R6", "rappdirs", "RColorBrewer", "rgl", "rlang", "rmarkdown", "S7", "sass", "scales", "tinytex", "vctrs", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "SingleCellTrajectoryAnalysis.Rmd", "filename": "SingleCellTrajectoryAnalysis.html", "title": "SingleCellTrajectoryAnalysis", "author": "Anna Laddach and Michael Shapiro", "engine": "knitr::rmarkdown", "headings": [ "SingleCellTrajectoryAnalysis", "Introduction", "Preparation", "The data", "Sampling a path", "Projecting path onto sphere and testing for directionality", "Sampling multiple paths", "Branch point analysis", "References" ], "created": "2020-07-13 15:32:36", "modified": "2021-01-13 13:46:05", "commits": 16 }, { "source": "TrajectoryGeometry.Rmd", "filename": "TrajectoryGeometry.html", "title": "TrajectoryGeometry", "author": "Anna Laddach and Michael Shapiro", "engine": "knitr::rmarkdown", "headings": [ "TrajectoryGeometry", "Introduction", "The Algorithm", "A Path gives points on a sphere", "How close are these points on the sphere?", "Testing for statistical significance", "Randomization", "Does a path confined to a direction consistently move in that direction?", "Stability" ], "created": "2020-04-13 18:46:06", "modified": "2024-02-20 10:51:41", "commits": 12 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "trajectorygeometry", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-07-03T16:19:57.000Z", "distro": "resolute", "commit": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "fileid": "https://r2.ropensci.org/a8428a9faae8a41a09c83ad424176908cafd117ded1292390a278b85c165de62", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28671903850" }, { "r": "4.6.1", "os": "linux", "version": "1.21.0", "date": "2026-07-03T16:20:02.000Z", "distro": "resolute", "commit": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "fileid": "https://r2.ropensci.org/583da01a9fa66c61eefec02e3ca1e2b269e67d115fcb0d3881cbd887ca6b7a91", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28671903850" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-07-03T16:18:57.000Z", "commit": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "fileid": "https://r2.ropensci.org/dc7bc7a348345726c324610545489f0d3650f43feaa3646509cab69c41ce46b8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28671903850" }, { "r": "4.6.1", "os": "mac", "version": "1.21.0", "date": "2026-07-03T16:18:50.000Z", "commit": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "fileid": "https://r2.ropensci.org/ed3cffdcc94a9c771f0fa1eb46290d8f3f5c4b4b15014f733b0a9b48eb69c196", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28671903850" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-07-03T16:19:35.000Z", "commit": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "fileid": "https://r2.ropensci.org/3ed8ad9a8ec746a61d5795c44763272cfd7ab00970e3d245a2e8ed23711da06e", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28671903850" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-07-03T16:18:12.000Z", "commit": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "fileid": "https://r2.ropensci.org/f65683908042a72e018682da297ee47c03836d487cc77e950ac302cc4a546434", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28671903850" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-07-03T16:18:12.000Z", "commit": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "fileid": "https://r2.ropensci.org/08fe57ca83822c0b90df0cad1069180f8a353a660bf858ff6368696660c3408a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28671903850" }, { "r": "4.6.1", "os": "win", "version": "1.21.0", "date": "2026-07-03T16:18:02.000Z", "commit": "3cb342384f217afa8d764cd76c18b1b65f4dd62c", "fileid": "https://r2.ropensci.org/79400a5546c04fcde902b3537e2937e5eaa1f46e2ed755680c9ce75621d4ac1d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28671903850" } ] }