{
  "_id": "6a129ed5acfb0bcc41d10062",
  "Package": "partCNV",
  "Type": "Package",
  "Title": "Infer locally aneuploid cells using single cell RNA-seq data",
  "Version": "1.10.0",
  "Authors@R": "c(\nperson(given=\"Ziyi\", family=\"Li\", email=\"zli16@mdanderson.org\", role=c(\"aut\", \"cre\", \"ctb\")),\nperson(given=\"Ruoxing\", family=\"Li\", email=\"ruoxingli@outlook.com\", role=\"ctb\"))",
  "Description": "This package uses a statistical framework for rapid and\naccurate detection of aneuploid cells with local copy number\ndeletion or amplification. Our method uses an EM algorithm with\nmixtures of Poisson distributions while incorporating\ncytogenetics information (e.g., regional deletion or\namplification) to guide the classification (partCNV). When\napplicable, we further improve the accuracy by integrating a\nHidden Markov Model for feature selection (partCNVH).",
  "Dependents": "R (>= 4.2.0)",
  "VignetteBuilder": "knitr",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "biocViews": "Software, CopyNumberVariation, HiddenMarkovModel,\nSingleCell, Classification",
  "Config/testthat/edition": "3",
  "PackageStatus": "Deprecated",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:57 UTC",
  "RemoteUrl": "https://github.com/bioc/partCNV",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "089046f7fa27905e2fdda74486a1dc60f63e3963",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-24 06:36:44 UTC",
    "User": "root"
  },
  "Author": "Ziyi Li [aut, cre, ctb],\nRuoxing Li [ctb]",
  "Maintainer": "Ziyi Li <zli16@mdanderson.org>",
  "MD5sum": "00a9dc1498f55bca618ae487a044d7a9",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "partCNV_1.10.0.tar.gz",
  "_fileid": "01d7cd58780d9e3ad951916ecbded5369add1eac3c22bf2fcb96b3ffaa9c5b59",
  "_filesize": 4551787,
  "_sha256": "01d7cd58780d9e3ad951916ecbded5369add1eac3c22bf2fcb96b3ffaa9c5b59",
  "_created": "2026-05-24T06:36:44.000Z",
  "_published": "2026-05-24T06:46:45.232Z",
  "_jobs": [
    {
      "job": 77577785152,
      "time": 209,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7182952395"
    },
    {
      "job": 77577785160,
      "time": 487,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7182979706"
    },
    {
      "job": 77577785166,
      "time": 515,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7182982560"
    },
    {
      "job": 77577785156,
      "time": 233,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7182981349"
    },
    {
      "job": 77577785164,
      "time": 269,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7182983176"
    },
    {
      "job": 77577491834,
      "time": 363,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7182931324"
    },
    {
      "job": 77577785163,
      "time": 181,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7182949493"
    },
    {
      "job": 77577785155,
      "time": 377,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7182968996"
    },
    {
      "job": 77577785165,
      "time": 320,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7182963022"
    },
    {
      "job": 77577785162,
      "time": 399,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7182971134"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354072611",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/partCNV",
  "_commit": {
    "id": "089046f7fa27905e2fdda74486a1dc60f63e3963",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381257
  },
  "_maintainer": {
    "name": "Ziyi Li",
    "email": "zli16@mdanderson.org",
    "login": "ziyili20",
    "description": "",
    "uuid": 24440640
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "depmixS4",
      "role": "Imports"
    },
    {
      "package": "Seurat",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "AnnotationHub",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "IRanges",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-14",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "software",
    "copynumbervariation",
    "hiddenmarkovmodel",
    "singlecell",
    "classification"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 272,
    "source": "https://www.bioconductor.org/packages/stats/bioc/partCNV"
  },
  "_searchresults": 5,
  "_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/partCNV.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "GetCytoLocation",
    "GetExprCountCyto",
    "NormalizeCounts",
    "partCNV",
    "partCNVH"
  ],
  "_datasets": [
    {
      "name": "Hg38_gtf",
      "title": "GTF data for Hg38 genome",
      "object": "Hg38_gtf",
      "file": "Hg38_gtf.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "seqnames",
        "start",
        "end",
        "gene_id",
        "gene_name"
      ],
      "rows": 36601,
      "table": true,
      "tojson": true
    },
    {
      "name": "SimData",
      "title": "Simulation data to examplify the usage of the method",
      "object": "SimData",
      "file": "SimData.RData",
      "class": [
        "dgCMatrix"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SimDataSce",
      "title": "Simulation SingleCellExperiment object to examplify the usage of the method",
      "object": "SimDataSce",
      "file": "SimDataSce.RData",
      "class": [
        "SingleCellExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "GetCytoLocation",
      "title": "Get exact location of the interested cytogenetics feature",
      "topics": [
        "GetCytoLocation"
      ]
    },
    {
      "page": "GetExprCountCyto",
      "title": "Get normalized gene expression counts for selected genes",
      "topics": [
        "GetExprCountCyto"
      ]
    },
    {
      "page": "Hg38_gtf",
      "title": "GTF data for Hg38 genome",
      "topics": [
        "Hg38_gtf"
      ]
    },
    {
      "page": "NormalizeCounts",
      "title": "Extract and normalize gene expression counts for a SingleCellExperiment object",
      "topics": [
        "NormalizeCounts"
      ]
    },
    {
      "page": "partCNV",
      "title": "Infer cells that are locally aneuploid using partCNV",
      "topics": [
        "partCNV"
      ]
    },
    {
      "page": "partCNVH",
      "title": "Infer cells that are locally aneuploid using partCNVH",
      "topics": [
        "partCNVH"
      ]
    },
    {
      "page": "SimData",
      "title": "Simulation data to examplify the usage of the method",
      "topics": [
        "SimData"
      ]
    },
    {
      "page": "SimDataSce",
      "title": "Simulation SingleCellExperiment object to examplify the usage of the method",
      "topics": [
        "SimDataSce"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/partCNV/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocManager",
    "BiocStyle",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bookdown",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "cluster",
    "codetools",
    "commonmark",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "deldir",
    "depmixS4",
    "digest",
    "dotCall64",
    "dplyr",
    "dqrng",
    "evaluate",
    "farver",
    "fastDummies",
    "fastmap",
    "filelock",
    "fitdistrplus",
    "FNN",
    "fontawesome",
    "fs",
    "future",
    "future.apply",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggrepel",
    "ggridges",
    "globals",
    "glue",
    "goftest",
    "gplots",
    "gridExtra",
    "gtable",
    "gtools",
    "here",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "ica",
    "igraph",
    "IRanges",
    "irlba",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "listenv",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "miniUI",
    "nlme",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "parallelly",
    "patchwork",
    "pbapply",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polyclip",
    "progressr",
    "promises",
    "purrr",
    "R6",
    "RANN",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppHNSW",
    "RcppProgress",
    "RcppTOML",
    "reshape2",
    "reticulate",
    "rlang",
    "rmarkdown",
    "ROCR",
    "rprojroot",
    "Rsolnp",
    "RSpectra",
    "RSQLite",
    "Rtsne",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scattermore",
    "sctransform",
    "Seqinfo",
    "Seurat",
    "SeuratObject",
    "shiny",
    "SingleCellExperiment",
    "sitmo",
    "sourcetools",
    "sp",
    "spam",
    "SparseArray",
    "spatstat.data",
    "spatstat.explore",
    "spatstat.geom",
    "spatstat.random",
    "spatstat.sparse",
    "spatstat.univar",
    "spatstat.utils",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tensor",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "truncnorm",
    "utf8",
    "uwot",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_score": 2.1760912590556813,
  "_indexed": false,
  "_nocasepkg": "partcnv",
  "_universes": [
    "bioc-release"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.10.0",
      "date": "2026-05-24T06:40:57.000Z",
      "distro": "noble",
      "commit": "089046f7fa27905e2fdda74486a1dc60f63e3963",
      "fileid": "f86dec494552324ebf24e7318fadd9d68bc4159387cf31d2048ccc6c0d598494",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354072611"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.10.0",
      "date": "2026-05-24T06:41:19.000Z",
      "distro": "noble",
      "commit": "089046f7fa27905e2fdda74486a1dc60f63e3963",
      "fileid": "1b9c3c6399edd4fa2a6ffba8b3231aa00ff1bf7b67dd1ddabbab510c3ad7f4e3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354072611"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.10.0",
      "date": "2026-05-24T06:43:18.000Z",
      "commit": "089046f7fa27905e2fdda74486a1dc60f63e3963",
      "fileid": "d500de097f49e1008aa73dc59fcc0f4caa1093f938dc69ac47f14aebf3958ab2",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354072611"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.10.0",
      "date": "2026-05-24T06:43:12.000Z",
      "commit": "089046f7fa27905e2fdda74486a1dc60f63e3963",
      "fileid": "c6bf4727790871867dd3e421e84527a2db38824d5816ab14f40b211cf4e166b3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354072611"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.10.0",
      "date": "2026-05-24T06:40:36.000Z",
      "commit": "089046f7fa27905e2fdda74486a1dc60f63e3963",
      "fileid": "65c208e0446cd4627510aee8f5cfc4c56fa394542ed725f0bbc4bdf0f42d3eaa",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354072611"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.10.0",
      "date": "2026-05-24T06:39:06.000Z",
      "commit": "089046f7fa27905e2fdda74486a1dc60f63e3963",
      "fileid": "ba93089cf4e33edf674700d5e169f491dfe2aa99ca5c1896560ae8ef6f279c10",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354072611"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.10.0",
      "date": "2026-05-24T06:39:17.000Z",
      "commit": "089046f7fa27905e2fdda74486a1dc60f63e3963",
      "fileid": "b29d8824c92f9d556841be1c034224a7afc234f2a9b46e9a06273d3428c0c648",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354072611"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.10.0",
      "date": "2026-05-24T06:39:16.000Z",
      "commit": "089046f7fa27905e2fdda74486a1dc60f63e3963",
      "fileid": "6d0e132906fe380a8b226edd960209b3bb38e6e92cffdfdcf97fb84b80ccbc83",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26354072611"
    }
  ]
}