{
  "_id": "6a1e97b01d7bb097a0a6d2b4",
  "Package": "uSORT",
  "Title": "uSORT: A self-refining ordering pipeline for gene selection",
  "Version": "1.39.0",
  "Author": "Mai Chan Lau, Hao Chen, Jinmiao Chen",
  "Description": "This package is designed to uncover the intrinsic cell\nprogression path from single-cell RNA-seq data. It incorporates\ndata pre-processing, preliminary PCA gene selection,\npreliminary cell ordering, feature selection, refined cell\nordering, and post-analysis interpretation and visualization.",
  "Maintainer": "Hao Chen <chen_hao@immunol.a-star.edu.sg>",
  "biocViews": "ImmunoOncology, RNASeq, GUI, CellBiology, DNASeq",
  "VignetteBuilder": "knitr",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "RoxygenNote": "5.0.1",
  "Config/pak/sysreqs": "libglpk-dev make libicu-dev libxml2-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:44:16 UTC",
  "RemoteUrl": "https://github.com/bioc/uSORT",
  "RemoteRef": "HEAD",
  "RemoteSha": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-02 08:37:01 UTC",
    "User": "root"
  },
  "MD5sum": "d695fe8b4232c06c688157cc2d061e9f",
  "_user": "bioc",
  "_type": "src",
  "_file": "uSORT_1.39.0.tar.gz",
  "_fileid": "f539dbfd4f6a9b2a4a03b621097ac7360386553fa1072dc165c0005c27a31893",
  "_filesize": 2900109,
  "_sha256": "f539dbfd4f6a9b2a4a03b621097ac7360386553fa1072dc165c0005c27a31893",
  "_created": "2026-06-02T08:37:01.000Z",
  "_published": "2026-06-02T08:43:28.414Z",
  "_jobs": [
    {
      "job": 79031826751,
      "time": 188,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7352947997"
    },
    {
      "job": 79031826634,
      "time": 317,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7352992229"
    },
    {
      "job": 79031826754,
      "time": 326,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7352996667"
    },
    {
      "job": 79031826595,
      "time": 172,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7352954529"
    },
    {
      "job": 79031826767,
      "time": 164,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7352964354"
    },
    {
      "job": 79031149371,
      "time": 239,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352882754"
    },
    {
      "job": 79031826712,
      "time": 143,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352932045"
    },
    {
      "job": 79031826694,
      "time": 214,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": ""
    },
    {
      "job": 79031826854,
      "time": 160,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7352938298"
    },
    {
      "job": 79031826907,
      "time": 222,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7352959602"
    }
  ],
  "_bioccheck": {
    "error": 3,
    "warning": 5,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26808220836",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/uSORT",
  "_commit": {
    "id": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
    "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": 1777380256
  },
  "_maintainer": {
    "name": "Hao Chen",
    "email": "chen_hao@immunol.a-star.edu.sg"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3.0",
      "role": "Depends"
    },
    {
      "package": "tcltk",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "RANN",
      "role": "Imports"
    },
    {
      "package": "RSpectra",
      "role": "Imports"
    },
    {
      "package": "VGAM",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "fpc",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "monocle",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.39.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.38.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "rnaseq",
    "gui",
    "cellbiology",
    "dnaseq"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 341,
    "source": "https://www.bioconductor.org/packages/stats/bioc/uSORT"
  },
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/uSORT.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "autoSPIN",
    "driving_force_gene_selection",
    "elbow_detection",
    "monocle_wrapper",
    "neighborhood_sortingcost",
    "pca_gene_selection",
    "Rwanderlust",
    "SPIN",
    "STS_sortingcost",
    "sWanderlust",
    "uSORT",
    "uSORT_GUI",
    "uSORT_preProcess",
    "uSORT_sorting_wrapper",
    "uSORT_write_results"
  ],
  "_help": [
    {
      "page": "autoSPIN",
      "title": "A wrapper function for autoSPIN sorting method",
      "topics": [
        "autoSPIN"
      ]
    },
    {
      "page": "clusterGenes1",
      "title": "A modified monocle's function",
      "topics": [
        "clusterGenes1"
      ]
    },
    {
      "page": "compareModels1",
      "title": "A modified monocle's function",
      "topics": [
        "compareModels1"
      ]
    },
    {
      "page": "diff_test_helper1",
      "title": "A modified monocle's helper function",
      "topics": [
        "diff_test_helper1"
      ]
    },
    {
      "page": "differentialGeneTest1",
      "title": "differential gene test",
      "topics": [
        "differentialGeneTest1"
      ]
    },
    {
      "page": "distance.function",
      "title": "A distance function A distance function computes cell-to-cell distance matrix.",
      "topics": [
        "distance.function"
      ]
    },
    {
      "page": "driving_force_gene_selection",
      "title": "A feature/ gene selection function",
      "topics": [
        "driving_force_gene_selection"
      ]
    },
    {
      "page": "elbow_detection",
      "title": "A elbow detection function",
      "topics": [
        "elbow_detection"
      ]
    },
    {
      "page": "EXP_to_CellDataSet",
      "title": "A function for constructing a Monocle's CellDataSet object from an expression matrix",
      "topics": [
        "EXP_to_CellDataSet"
      ]
    },
    {
      "page": "fluidigmSC_analyzeGeneDetection",
      "title": "A gene detection function",
      "topics": [
        "fluidigmSC_analyzeGeneDetection"
      ]
    },
    {
      "page": "fluidigmSC_identifyExpOutliers",
      "title": "An outlier detection function",
      "topics": [
        "fluidigmSC_identifyExpOutliers"
      ]
    },
    {
      "page": "fluidigmSC_isElementIgnoreCase",
      "title": "A gene finding function",
      "topics": [
        "fluidigmSC_isElementIgnoreCase"
      ]
    },
    {
      "page": "fluidigmSC_readLinearExp",
      "title": "An expression reading function",
      "topics": [
        "fluidigmSC_readLinearExp"
      ]
    },
    {
      "page": "fluidigmSC_removeGenesByLinearExpForAllType",
      "title": "A gene trimming function",
      "topics": [
        "fluidigmSC_removeGenesByLinearExpForAllType"
      ]
    },
    {
      "page": "fluidigmSC_removeGenesByLinearExpForAllType_log2",
      "title": "A gene trimming function",
      "topics": [
        "fluidigmSC_removeGenesByLinearExpForAllType_log2"
      ]
    },
    {
      "page": "monocle_wrapper",
      "title": "A wrapper function for Monocle sorting method",
      "topics": [
        "monocle_wrapper"
      ]
    },
    {
      "page": "neighborhood_sorting",
      "title": "A sorting function using the Neighborhood algorithm",
      "topics": [
        "neighborhood_sorting"
      ]
    },
    {
      "page": "neighborhood_sorting_wrapper",
      "title": "A wrapper function for Neighborhood sorting.",
      "topics": [
        "neighborhood_sorting_wrapper"
      ]
    },
    {
      "page": "neighborhood_sortingcost",
      "title": "A cost computation function for Neighborhood algorithm",
      "topics": [
        "neighborhood_sortingcost"
      ]
    },
    {
      "page": "pca_gene_selection",
      "title": "Gene selection using PCA technique",
      "topics": [
        "pca_gene_selection"
      ]
    },
    {
      "page": "Rwanderlust",
      "title": "R inplementation of wanderlust",
      "topics": [
        "Rwanderlust"
      ]
    },
    {
      "page": "scattering_quantification_per_gene",
      "title": "An expression scattering measurement function",
      "topics": [
        "scattering_quantification_per_gene"
      ]
    },
    {
      "page": "sorting_method_parameter_GUI",
      "title": "GUI for sorting method paramters",
      "topics": [
        "sorting_method_parameter_GUI"
      ]
    },
    {
      "page": "SPIN",
      "title": "A wrapper function for SPIN sorting method",
      "topics": [
        "SPIN"
      ]
    },
    {
      "page": "STS_sorting",
      "title": "A sorting function using the Side-to-Side (STS) algorithm",
      "topics": [
        "STS_sorting"
      ]
    },
    {
      "page": "STS_sorting_wrapper",
      "title": "A wrapper function for Side-to-Side (STS) sorting.",
      "topics": [
        "STS_sorting_wrapper"
      ]
    },
    {
      "page": "STS_sortingcost",
      "title": "A cost computation function for Side-to-Side (STS) algorithm",
      "topics": [
        "STS_sortingcost"
      ]
    },
    {
      "page": "summed_local_variance",
      "title": "A summed local variance function",
      "topics": [
        "summed_local_variance"
      ]
    },
    {
      "page": "summed_local_variance_cyclical",
      "title": "A summed local variance function for cyclical linear data type",
      "topics": [
        "summed_local_variance_cyclical"
      ]
    },
    {
      "page": "summed_local_variance_linear",
      "title": "A summed local variance function for strictly linear data type",
      "topics": [
        "summed_local_variance_linear"
      ]
    },
    {
      "page": "sWanderlust",
      "title": "sWanderlust",
      "topics": [
        "sWanderlust"
      ]
    },
    {
      "page": "trajectory_landmarks",
      "title": "determining initial trajectory and landmarks",
      "topics": [
        "trajectory_landmarks"
      ]
    },
    {
      "page": "uSORT",
      "title": "uSORT: A self-refining ordering pipeline for gene selection",
      "topics": [
        "uSORT-package",
        "uSORT"
      ]
    },
    {
      "page": "uSORT_GUI",
      "title": "The user friendly GUI for 'uSORT-package'",
      "topics": [
        "uSORT_GUI"
      ]
    },
    {
      "page": "uSORT_parameters_GUI",
      "title": "The GUI for inputting paramters for uSORT",
      "topics": [
        "uSORT_parameters_GUI"
      ]
    },
    {
      "page": "uSORT_preProcess",
      "title": "A data loading and pre-processing function",
      "topics": [
        "uSORT_preProcess"
      ]
    },
    {
      "page": "uSORT_sorting_wrapper",
      "title": "wrapper of all avaliable sorting methods in uSORT",
      "topics": [
        "uSORT_sorting_wrapper"
      ]
    },
    {
      "page": "uSORT_write_results",
      "title": "Resluts parsing for uSORT",
      "topics": [
        "uSORT_write_results"
      ]
    },
    {
      "page": "variability_per_gene",
      "title": "A utility function for scattering_quantification_per_gene",
      "topics": [
        "variability_per_gene"
      ]
    },
    {
      "page": "wanderlust_wrapper",
      "title": "a wrapper of wanderlust for sWanderlust",
      "topics": [
        "wanderlust_wrapper"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "biocViews",
    "bitops",
    "caTools",
    "class",
    "cli",
    "cluster",
    "combinat",
    "cpp11",
    "DDRTree",
    "DEoptimR",
    "diptest",
    "dplyr",
    "farver",
    "fastICA",
    "flexmix",
    "fpc",
    "generics",
    "ggplot2",
    "glue",
    "gplots",
    "graph",
    "gridExtra",
    "gtable",
    "gtools",
    "HSMMSingleCell",
    "igraph",
    "irlba",
    "isoband",
    "kernlab",
    "KernSmooth",
    "labeling",
    "lattice",
    "leidenbase",
    "lifecycle",
    "limma",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixStats",
    "mclust",
    "modeltools",
    "monocle",
    "nnet",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
    "prabclus",
    "proxy",
    "R6",
    "RANN",
    "RBGL",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RCurl",
    "reshape2",
    "rlang",
    "robustbase",
    "RSpectra",
    "Rtsne",
    "RUnit",
    "S7",
    "scales",
    "slam",
    "statmod",
    "stringi",
    "stringr",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "VGAM",
    "viridis",
    "viridisLite",
    "withr",
    "XML"
  ],
  "_vignettes": [
    {
      "source": "uSORT_quick_start.Rmd",
      "filename": "uSORT_quick_start.html",
      "title": "uSORT: Quick Start",
      "engine": "knitr::rmarkdown",
      "headings": [
        "uSORT workflow",
        "Run uSORT",
        "uSORT GUI",
        "uSORT Main Function",
        "uSORT Example",
        "Result Object and files",
        "Preliminary ordering heatmap with signature gene",
        "Refine ordering heatmap with signature gene",
        "Session Information"
      ],
      "created": "2016-10-02 20:42:18",
      "modified": "2016-10-02 20:42:18",
      "commits": 1
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "usort",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.39.0",
      "date": "2026-05-03T16:12:09.000Z",
      "commit": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
      "fileid": "cf753770fff747c0ffcedf88aa424e407f2071d2239efe31a04b972863cc5d53",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25283798505"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.39.0",
      "date": "2026-06-02T08:40:18.000Z",
      "distro": "noble",
      "commit": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
      "fileid": "39b6d046e4460c6fc710943fc10d71befaa6c3fb1fdaf959b88efecdee510d6b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808220836"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.39.0",
      "date": "2026-06-02T08:40:27.000Z",
      "distro": "noble",
      "commit": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
      "fileid": "6b9e5f9774d38a4b6dd210205845ab4244595741635982bdef0933db8162b485",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808220836"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.39.0",
      "date": "2026-06-02T08:39:37.000Z",
      "commit": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
      "fileid": "35a12e87e8392f8776dc22ce2b516c60296aca4613b36b6169266a89c0ef6c99",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808220836"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.39.0",
      "date": "2026-06-02T08:40:08.000Z",
      "commit": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
      "fileid": "7618046328c7c34fe0355ca11e3b80a06649f11f9e7fcc31d25c540eb88ba833",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808220836"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.39.0",
      "date": "2026-06-02T08:39:56.000Z",
      "commit": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
      "fileid": "feb6f0a6b7ca8573ed2132bc53f7f83411b01c735968c4a5640cfa61237f589f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808220836"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.39.0",
      "date": "2026-06-02T08:39:08.000Z",
      "commit": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
      "fileid": "c80f635e0995a0023ccb9f9dd578c0b3f48a0cb350ecb9efc8ec3e6d5cefca53",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808220836"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.39.0",
      "date": "2026-06-02T08:39:11.000Z",
      "commit": "ea64dabbac25db00016f1fc0b205778ff591cc0a",
      "fileid": "72cf97964bbd80711c6b24de0cba97a0887e1e12de70e366626d7455ab71cb13",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808220836"
    }
  ]
}