{
  "_id": "6a49483da788432aeabf41ef",
  "Package": "velociraptor",
  "Title": "Toolkit for Single-Cell Velocity",
  "Version": "1.23.0",
  "Date": "2026-04-15",
  "Authors@R": "c(person(\"Kevin\", \"Rue-Albrecht\", role = c(\"aut\", \"cre\"), email = \"kevinrue67@gmail.com\", comment = c(ORCID = \"0000-0003-3899-3872\")),\nperson(\"Aaron\", \"Lun\", role=\"aut\", email=\"infinite.monkeys.with.keyboards@gmail.com\", comment = c(ORCID = '0000-0002-3564-4813')),\nperson(\"Charlotte\", \"Soneson\", role=\"aut\", email=\"charlottesoneson@gmail.com\", comment = c(ORCID = '0000-0003-3833-2169')),\nperson(\"Michael\", \"Stadler\", role=\"aut\", email=\"michael.stadler@fmi.ch\", comment = c(ORCID = '0000-0002-2269-4934')))",
  "Description": "This package provides Bioconductor-friendly wrappers for\nRNA velocity calculations in single-cell RNA-seq data. We use\nthe basilisk package to manage Conda environments, and the\nzellkonverter package to convert data structures between\nSingleCellExperiment (R) and AnnData (Python). The information\nproduced by the velocity methods is stored in the various\ncomponents of the SingleCellExperiment class.",
  "StagedInstall": "no",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "URL": "https://github.com/kevinrue/velociraptor",
  "BugReports": "https://github.com/kevinrue/velociraptor/issues",
  "biocViews": "SingleCell, GeneExpression, Sequencing, Coverage",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libpng-dev python3 zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:53:48 UTC",
  "RemoteUrl": "https://github.com/bioc/velociraptor",
  "RemoteRef": "HEAD",
  "RemoteSha": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-03 09:45:42 UTC",
    "User": "root"
  },
  "Author": "Kevin Rue-Albrecht [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3899-3872>),\nAaron Lun [aut] (ORCID: <https://orcid.org/0000-0002-3564-4813>),\nCharlotte Soneson [aut] (ORCID:\n<https://orcid.org/0000-0003-3833-2169>),\nMichael Stadler [aut] (ORCID: <https://orcid.org/0000-0002-2269-4934>)",
  "Maintainer": "Kevin Rue-Albrecht <kevinrue67@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "velociraptor_1.23.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d002bb084f997e5fe2b1d43d34ed78efc1723cef21ee424a02a93f484401baf9",
  "_filesize": 692472,
  "_sha256": "d002bb084f997e5fe2b1d43d34ed78efc1723cef21ee424a02a93f484401baf9",
  "_expires": "2026-10-12T17:51:55.000Z",
  "_created": "2026-07-03T09:45:42.000Z",
  "_published": "2026-07-04T17:51:57.400Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 6
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28651379050",
  "_status": "success",
  "_upstream": "https://github.com/bioc/velociraptor",
  "_commit": {
    "id": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380828
  },
  "_maintainer": {
    "name": "Kevin Rue-Albrecht",
    "email": "kevinrue67@gmail.com",
    "login": "kevinrue",
    "mastodon": "@kevinrue@fosstodon.org",
    "orcid": "0000-0003-3899-3872",
    "description": "Ingénieur diplômé;\nComputational Biologist; \nSoftware engineer;\nBioconductor contributor",
    "uuid": 5769108
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85153825705,
      "time": 258,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8063334154"
    },
    {
      "job": 85153825611,
      "time": 1360,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8063727244"
    },
    {
      "job": 85153825822,
      "time": 1312,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8063710370"
    },
    {
      "job": 85153825672,
      "time": 785,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8063516900"
    },
    {
      "job": 85153825615,
      "time": 796,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8063520952"
    },
    {
      "job": 85153825528,
      "time": 1271,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8063243760"
    },
    {
      "job": 85153825825,
      "time": 263,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8063336184"
    },
    {
      "job": 85153825657,
      "time": 1571,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8063800980"
    },
    {
      "job": 85153825810,
      "time": 1547,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8063791397"
    },
    {
      "job": 85153825748,
      "time": 1621,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8063818048"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "reticulate",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "DelayedArray",
      "role": "Imports"
    },
    {
      "package": "basilisk",
      "role": "Imports"
    },
    {
      "package": "zellkonverter",
      "role": "Imports"
    },
    {
      "package": "scuttle",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "BiocSingular",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "pkgdown",
      "role": "Suggests"
    },
    {
      "package": "scran",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    },
    {
      "package": "Rtsne",
      "role": "Suggests"
    },
    {
      "package": "graphics",
      "role": "Suggests"
    },
    {
      "package": "grDevices",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "GGally",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "metR",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-28",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-16",
      "n": 3
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.22.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "singlecell",
    "geneexpression",
    "sequencing",
    "coverage",
    "rna-velocity"
  ],
  "_stars": 61,
  "_contributors": [
    {
      "user": "kevinrue",
      "count": 57,
      "uuid": 5769108
    },
    {
      "user": "ltla",
      "count": 28,
      "uuid": 8166669
    },
    {
      "user": "csoneson",
      "count": 15,
      "uuid": 5628952
    },
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 8,
      "uuid": 2746443
    },
    {
      "user": "federicomarini",
      "count": 1,
      "uuid": 7447478
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    },
    {
      "user": "multimeric",
      "count": 1,
      "uuid": 5019367
    },
    {
      "user": "mbstadler",
      "count": 1,
      "uuid": 13657342
    },
    {
      "user": "ttriche",
      "count": 1,
      "uuid": 4386
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/kevinrue/velociraptor",
  "_searchresults": 61,
  "_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/velociraptor.html",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/kevinrue/velociraptor",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".grid_vectors",
    "embedVelocity",
    "gridVectors",
    "plotVelocity",
    "plotVelocityStream",
    "scvelo"
  ],
  "_help": [
    {
      "page": "embedVelocity",
      "title": "Project velocities onto an embedding",
      "topics": [
        "embedVelocity",
        "embedVelocity,ANY-method",
        "embedVelocity,SingleCellExperiment-method"
      ]
    },
    {
      "page": "gridVectors",
      "title": "Summarize vectors into a grid",
      "topics": [
        "gridVectors",
        "gridVectors,ANY-method",
        "gridVectors,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotVelocity",
      "title": "Phase and velocity graphs for a set of genes",
      "topics": [
        "plotVelocity"
      ]
    },
    {
      "page": "plotVelocityStream",
      "title": "Velocity stream plot in low-dimensional space",
      "topics": [
        "plotVelocityStream"
      ]
    },
    {
      "page": "scvelo",
      "title": "RNA velocity with 'scVelo'",
      "topics": [
        "scvelo",
        "scvelo,ANY-method",
        "scvelo,SingleCellExperiment-method",
        "scvelo,SummarizedExperiment-method"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/velociraptor/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/velociraptor/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "assorthead",
    "basilisk",
    "beachmat",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "BiocSingular",
    "cli",
    "codetools",
    "cpp11",
    "DelayedArray",
    "dir.expiry",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "here",
    "IRanges",
    "irlba",
    "jsonlite",
    "lambda.r",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "png",
    "rappdirs",
    "Rcpp",
    "RcppTOML",
    "reticulate",
    "rlang",
    "rprojroot",
    "rsvd",
    "S4Arrays",
    "S4Vectors",
    "ScaledMatrix",
    "scuttle",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "withr",
    "XVector",
    "zellkonverter"
  ],
  "_vignettes": [
    {
      "source": "velociraptor.Rmd",
      "filename": "velociraptor.html",
      "title": "Computing RNA velocity in a Bioconductor framework",
      "author": "Kevin Rue-Albrecht, Aaron Lun, Charlotte Soneson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Downsampling for demonstration",
        "Basic workflow",
        "Advanced options",
        "Session information",
        "References"
      ],
      "created": "2021-02-22 09:40:39",
      "modified": "2024-05-30 08:03:04",
      "commits": 4
    }
  ],
  "_score": 7.825932175124841,
  "_indexed": true,
  "_nocasepkg": "velociraptor",
  "_universes": [
    "bioc",
    "kevinrue"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-07-03T09:50:25.000Z",
      "distro": "resolute",
      "commit": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
      "fileid": "https://r2.ropensci.org/6318ff0a62a6fa1dc77ab7dd67cce35a60d716e9ef55ed1e7726085db66c2075",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28651379050"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.23.0",
      "date": "2026-07-03T09:50:48.000Z",
      "distro": "resolute",
      "commit": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
      "fileid": "https://r2.ropensci.org/13dfdc8bc10dd5c73f16a598ccd3d052f9038509aa24c7ae67ed279ce00955eb",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28651379050"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-07-03T09:48:22.000Z",
      "commit": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
      "fileid": "https://r2.ropensci.org/df436ceb73debf2048dd03b10bd0ec46c87a46a12c12d7b0290c17a458c0e1e9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28651379050"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.23.0",
      "date": "2026-07-03T09:48:35.000Z",
      "commit": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
      "fileid": "https://r2.ropensci.org/93d6ecb5c70aa33d5d96a696dfbc9bfa647fe481a542db38c1b8b3c01805afed",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28651379050"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.23.0",
      "date": "2026-07-03T09:50:32.000Z",
      "commit": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
      "fileid": "https://r2.ropensci.org/2d0af021eb1fe1db5ed1fe9ae0700254073f5b9dddb081298d00d5f7c7402d00",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28651379050"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-07-03T10:05:35.000Z",
      "commit": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
      "fileid": "https://r2.ropensci.org/8768eaf973eec1798c9990a5537f3e56d16aaf5ba4de18f1d5d07f8793074d38",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28651379050"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-07-03T10:04:57.000Z",
      "commit": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
      "fileid": "https://r2.ropensci.org/ed41e51493ea5c762247c58de6e028b5a34b31de29dcd715c4368df50898c036",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28651379050"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.23.0",
      "date": "2026-07-03T10:05:56.000Z",
      "commit": "280d0504ed558a72211ecaf76e0f5bb74f55b60c",
      "fileid": "https://r2.ropensci.org/cbe30cba16b9ac228f338c3970f1880e07b96e0d4e44b2c3881d7b810ee7c567",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28651379050"
    }
  ]
}