{ "_id": "6ae7446a1e2c7b3a4f52feb0", "Package": "TrajectoryUtils", "Version": "1.21.0", "Date": "2024-02-03", "Title": "Single-Cell Trajectory Analysis Utilities", "Description": "Implements low-level utilities for single-cell trajectory\nanalysis, primarily intended for re-use inside higher-level\npackages. Include a function to create a cluster-level minimum\nspanning tree and data structures to hold pseudotime inference\nresults.", "Authors@R": "c(\nperson(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\"), email=\"infinite.monkeys.with.keyboards@gmail.com\"),\nperson(\"Kelly\", \"Street\", role=\"aut\")\n)", "License": "GPL-3", "biocViews": "GeneExpression, SingleCell", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.1", "BugReports": "https://github.com/LTLA/TrajectoryUtils/issues", "URL": "https://bioconductor.org/packages/TrajectoryUtils", "Config/pak/sysreqs": "libglpk-dev libxml2-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:54:55 UTC", "RemoteUrl": "https://github.com/bioc/TrajectoryUtils", "RemoteRef": "HEAD", "RemoteSha": "79012de5a31255225db9e983373900b5ccb5ce6b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 12:55:32 UTC", "User": "root" }, "Author": "Aaron Lun [aut, cre],\nKelly Street [aut]", "Maintainer": "Aaron Lun ", "_user": "bioc", "_type": "src", "_file": "TrajectoryUtils_1.21.0.tar.gz", "_fileid": "https://r2.ropensci.org/b7007fa7e1b89bf16ea11de1b67c7664805b2f2486f4b6aa21c1c9d503d75f0c", "_filesize": 207252, "_sha256": "b7007fa7e1b89bf16ea11de1b67c7664805b2f2486f4b6aa21c1c9d503d75f0c", "_expires": "2027-02-09T13:53:44.000Z", "_created": "2026-11-01T12:55:32.000Z", "_published": "2026-11-01T13:53:46.542Z", "_upstream": "https://github.com/bioc/TrajectoryUtils", "_status": "success", "_maintainer": { "name": "Aaron Lun", "email": "infinite.monkeys.with.keyboards@gmail.com", "login": "ltla", "twitter": "@realAaronLun", "description": "(ノಠ益ಠ)ノ彡┻━┻\n", "uuid": 8166669 }, "_jobs": [ { "job": 124854711200, "time": 166, "config": "bioc-checks", "r": "4.6.2", "check": "WARNING", "artifact": "13085001004" }, { "job": 124854711251, "time": 359, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13084941773" }, { "job": 124854711292, "time": 293, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13085155812" }, { "job": 124854711280, "time": 209, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13085382352" }, { "job": 124854711224, "time": 216, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13085044039" }, { "job": 124853855204, "time": 229, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13083964292" }, { "job": 124854711307, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13084138072" }, { "job": 124854711346, "time": 232, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13084856651" }, { "job": 124854711266, "time": 154, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13084109660" }, { "job": 124854711376, "time": 213, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13084647023" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41308505086", "_commit": { "id": "79012de5a31255225db9e983373900b5ccb5ce6b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380895 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "SingleCellExperiment", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocNeighbors", "role": "Suggests" }, { "package": "DelayedArray", "role": "Suggests" }, { "package": "DelayedMatrixStats", "role": "Suggests" }, { "package": "BiocParallel", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 9, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "geneexpression", "singlecell" ], "_stars": 1, "_contributors": [ { "user": "ltla", "count": 36, "uuid": 8166669 }, { "user": "nturaga", "count": 6, "uuid": 2746443 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "kstreet13", "count": 1, "uuid": 11052277 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 6199, "source": "https://www.bioconductor.org/packages/stats/bioc/TrajectoryUtils" }, "_devurl": "https://github.com/ltla/trajectoryutils", "_searchresults": 23, "_abi": { "exports": [ { "key": "TrajectoryUtils::PseudotimeOrdering", "hash": "371264e81b734ca7" }, { "key": "TrajectoryUtils::generic:cellData<-", "hash": "505cdc86e1faaec9" }, { "key": "TrajectoryUtils::generic:cellnames<-", "hash": "032e7629cc22ee91" }, { "key": "TrajectoryUtils::generic:createClusterMST", "hash": "eaaed696a9327a53" }, { "key": "TrajectoryUtils::generic:pathData<-", "hash": "2134ef6cd2d0217f" }, { "key": "TrajectoryUtils::generic:pathStat<-", "hash": "2c8935730eee4e5e" }, { "key": "TrajectoryUtils::generic:pathStatNames<-", "hash": "872993a7010de702" }, { "key": "TrajectoryUtils::generic:pathStats<-", "hash": "b6095e5dce8d5f38" }, { "key": "TrajectoryUtils::generic:pathnames<-", "hash": "1ddbf16abe76e99d" } ], "imports": [ { "key": "S4Vectors::Annotated", "hash": "9b5b8ee6ad9969f8" }, { "key": "S4Vectors::RectangularData", "hash": "d414a10823a4aada" }, { "key": "S4Vectors::Vector", "hash": "09cab0bd77ae353b" }, { "key": "S4Vectors::vector_OR_Vector", "hash": "f3fc18c9f8ff2633" }, { "key": "SummarizedExperiment::SummarizedExperiment", "hash": "d53ca73257d1e8cf" } ] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/TrajectoryUtils.html" ], "_homeurl": "https://github.com/ltla/trajectoryutils", "_realowner": "bioc", "_cranurl": false, "_exports": [ "averagePseudotime", "cellData", "cellData<-", "cellnames", "cellnames<-", "createClusterMST", "defineMSTPaths", "guessMSTRoots", "ncells", "npaths", "pathData", "pathData<-", "pathnames", "pathnames<-", "pathStat", "pathStat<-", "pathStatNames", "pathStatNames<-", "pathStats", "pathStats<-", "PseudotimeOrdering", "rowmean", "rowmedian", "show", "splitByBranches" ], "_help": [ { "page": "averagePseudotime", "title": "Compute the average pseudotime", "topics": [ "averagePseudotime" ] }, { "page": "createClusterMST", "title": "Minimum spanning trees on cluster centroids", "topics": [ "createClusterMST", "createClusterMST,ANY-method", "createClusterMST,SingleCellExperiment-method", "createClusterMST,SummarizedExperiment-method" ] }, { "page": "defineMSTPaths", "title": "Define paths through the MST", "topics": [ "defineMSTPaths" ] }, { "page": "guessMSTRoots", "title": "Guess the roots of a MST", "topics": [ "guessMSTRoots" ] }, { "page": "PseudotimeOrdering", "title": "The PseudotimeOrdering class", "topics": [ "$,PseudotimeOrdering-method", "$<-,PseudotimeOrdering-method", "cellData", "cellData<-", "cellData<-,PseudotimeOrdering-method", "cellnames", "cellnames<-", "cellnames<-,PseudotimeOrdering-method", "ncells", "npaths", "pathData", "pathData<-", "pathData<-,PseudotimeOrdering-method", "pathnames", "pathnames<-", "pathnames<-,PseudotimeOrdering-method", "pathStat", "pathStat<-", "pathStat<-,PseudotimeOrdering-method", "pathStatNames", "pathStatNames<-", "pathStatNames<-,PseudotimeOrdering-method", "pathStats", "pathStats<-", "pathStats<-,PseudotimeOrdering-method", "PseudotimeOrdering", "PseudotimeOrdering-class", "show,PseudotimeOrdering-method" ] }, { "page": "rowmean", "title": "Compute column means based on a grouping variable", "topics": [ "rowmean", "rowmedian" ] }, { "page": "splitByBranches", "title": "Split a graph into branch-free paths", "topics": [ "splitByBranches" ] } ], "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "cpp11", "DelayedArray", "generics", "GenomicRanges", "glue", "igraph", "IRanges", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "pkgconfig", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "vctrs", "XVector" ], "_vignettes": [ { "source": "overview.Rmd", "filename": "overview.html", "title": "Trajectory utilities for package developers", "author": "Aaron Lun", "engine": "knitr::rmarkdown", "headings": [ "Overview", "MST construction", "Operations on the MST", "The PseudotimeOrdering class", "Session information" ], "created": "2020-11-09 06:49:17", "modified": "2020-11-30 02:28:32", "commits": 3 } ], "_score": 6.363564486911797, "_indexed": true, "_nocasepkg": "trajectoryutils", "_universes": [ "bioc", "ltla" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-11-01T13:04:52.000Z", "distro": "resolute", "commit": "79012de5a31255225db9e983373900b5ccb5ce6b", "fileid": "https://r2.ropensci.org/50e55e9fcdfbae4623f1882f78d828e7cb902c1ed1562ab3a068d54202969b2e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308505086" }, { "r": "4.6.2", "os": "linux", "version": "1.21.0", "date": "2026-11-01T13:04:15.000Z", "distro": "resolute", "commit": "79012de5a31255225db9e983373900b5ccb5ce6b", "fileid": "https://r2.ropensci.org/af496e1e5b91f5e5a9e66c7d8efc7341eec7c58625a9476f4d9fae5a8be6822f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308505086" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-11-01T13:22:52.000Z", "commit": "79012de5a31255225db9e983373900b5ccb5ce6b", "fileid": "https://r2.ropensci.org/308d8f7bf3e82ee5bd77a03d8291fb6dae7ee5066c27000a6cdacdf2f046337f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308505086" }, { "r": "4.6.2", "os": "mac", "version": "1.21.0", "date": "2026-11-01T13:22:40.000Z", "commit": "79012de5a31255225db9e983373900b5ccb5ce6b", "fileid": "https://r2.ropensci.org/f95cc06699bca8e0c826970c99d81243adf244a15a0531cf1062c87e5ea52631", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308505086" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-11-01T13:03:26.000Z", "commit": "79012de5a31255225db9e983373900b5ccb5ce6b", "fileid": "https://r2.ropensci.org/f40f7b4c3d504d4ce4e847957cf4163cbc69df1edc98c86e035b0816f2ef6615", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308505086" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-11-01T13:02:31.000Z", "commit": "79012de5a31255225db9e983373900b5ccb5ce6b", "fileid": "https://r2.ropensci.org/4e9cdd410125df6d3ccda8bab0f20528cd34e98f6e64570791997b27291ced93", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308505086" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-11-01T13:02:10.000Z", "commit": "79012de5a31255225db9e983373900b5ccb5ce6b", "fileid": "https://r2.ropensci.org/1f9b4058ce73f7b5f317e0e0119a59a4da5c76b1d62f810c2cb46427e6b42ba2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308505086" }, { "r": "4.6.2", "os": "win", "version": "1.21.0", "date": "2026-11-01T13:02:41.000Z", "commit": "79012de5a31255225db9e983373900b5ccb5ce6b", "fileid": "https://r2.ropensci.org/864b0fd824537cf808f759d3e71d2e5bfa9c295be61e100ae4864556ded7e3f3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308505086" } ] }