{
  "_id": "6a17e0e5acfb0bcc41d9efd2",
  "Package": "DeMixT",
  "Title": "Cell type-specific deconvolution of heterogeneous tumor samples\nwith two or three components using expression data from RNAseq\nor microarray platforms",
  "Version": "2.1.0",
  "Date": "2026-03-20",
  "Authors@R": "c(\nperson(\"Zeya\", \"Wang\", email = \"zw17.rice@gmail.com\", role = c(\"aut\")),\nperson(\"Shaolong\", \"Cao\", email = \"scao@mdanderson.org\", role = c(\"aut\")),\nperson(\"Liyang\", \"Xie\", email = \"xieliyang@utexas.edu\", role = c(\"aut\")),\nperson(\"Ruonan\", \"Li\", email = \"RLi10@mdanderson.org\", role = c(\"cre\")),\nperson(\"Wenyi\", \"Wang\", email = \"wwang7@mdanderson.org\", role = c(\"aut\"))\n)",
  "Description": "DeMixT is a software package that performs deconvolution\non transcriptome data from a mixture of two or three\ncomponents.",
  "LazyData": "TRUE",
  "NeedsCompilation": "yes",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, StatisticalMethod, Classification, GeneExpression,\nSequencing, Microarray, TissueMicroarray, Coverage",
  "License": "GPL-3",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:51 UTC",
  "RemoteUrl": "https://github.com/bioc/DeMixT",
  "RemoteRef": "HEAD",
  "RemoteSha": "7874c43e7a22a104026e39df894e2d52f92971ba",
  "Packaged": {
    "Date": "2026-05-28 06:20:02 UTC",
    "User": "root"
  },
  "Author": "Zeya Wang [aut],\nShaolong Cao [aut],\nLiyang Xie [aut],\nRuonan Li [cre],\nWenyi Wang [aut]",
  "Maintainer": "Ruonan Li <RLi10@mdanderson.org>",
  "MD5sum": "5fc3a03b0112d4f719b58647b9e6f667",
  "_user": "bioc",
  "_type": "src",
  "_file": "DeMixT_2.1.0.tar.gz",
  "_fileid": "3ad3fba19e45d11cb4707e18716722883aa4c9380f2b58d9e63c930d60bd6f5a",
  "_filesize": 11238950,
  "_sha256": "3ad3fba19e45d11cb4707e18716722883aa4c9380f2b58d9e63c930d60bd6f5a",
  "_created": "2026-05-28T06:20:02.000Z",
  "_published": "2026-05-28T06:29:57.302Z",
  "_jobs": [
    {
      "job": 78235212932,
      "time": 202,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7259074373"
    },
    {
      "job": 78235212963,
      "time": 319,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259101710"
    },
    {
      "job": 78235212968,
      "time": 415,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259124327"
    },
    {
      "job": 78235212957,
      "time": 313,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259099992"
    },
    {
      "job": 78235212986,
      "time": 381,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259116215"
    },
    {
      "job": 78235213097,
      "time": 198,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259086467"
    },
    {
      "job": 78235212972,
      "time": 445,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259148955"
    },
    {
      "job": 78235212977,
      "time": 221,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259094620"
    },
    {
      "job": 78235212974,
      "time": 466,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259142506"
    },
    {
      "job": 78234628066,
      "time": 302,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259027055"
    },
    {
      "job": 78235212964,
      "time": 180,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259069448"
    },
    {
      "job": 78235213057,
      "time": 418,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259124662"
    },
    {
      "job": 78235212930,
      "time": 449,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259132000"
    },
    {
      "job": 78235212940,
      "time": 439,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259129923"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 18
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/DeMixT",
  "_commit": {
    "id": "7874c43e7a22a104026e39df894e2d52f92971ba",
    "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": 1777380591
  },
  "_maintainer": {
    "name": "Ruonan Li",
    "email": "rli10@mdanderson.org"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "parallel",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.0",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "truncdist",
      "role": "Imports"
    },
    {
      "package": "base64enc",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "KernSmooth",
      "role": "Imports"
    },
    {
      "package": "matrixcalc",
      "role": "Imports"
    },
    {
      "package": "sva",
      "role": "Imports"
    },
    {
      "package": "dendextend",
      "role": "Imports"
    },
    {
      "package": "fitdistrplus",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "psych",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "calibrate",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-13",
      "n": 3
    },
    {
      "week": "2026-14",
      "n": 3
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.1.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "statisticalmethod",
    "classification",
    "geneexpression",
    "sequencing",
    "microarray",
    "tissuemicroarray",
    "coverage",
    "cpp",
    "openmp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 395,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DeMixT"
  },
  "_mentions": 5,
  "_searchresults": 30,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DeMixT.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "batch_correction",
    "DeMixNB",
    "DeMixNB_preprocessing",
    "DeMixT",
    "DeMixT_DE",
    "DeMixT_GS",
    "DeMixT_preprocessing",
    "DeMixT_S2",
    "detect_suspicious_sample_by_hierarchical_clustering_2comp",
    "gene_selection_DE",
    "Optimum_KernelC",
    "plot_dim",
    "plot_sd",
    "scale_normalization_75th_percentile",
    "simulate_2comp",
    "simulate_3comp",
    "subset_sd",
    "subset_sd_gene_remaining"
  ],
  "_datasets": [
    {
      "name": "test.data.2comp",
      "title": "Simulated two-component test data",
      "object": "test.data.2comp",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "test.data.3comp",
      "title": "Simulated three-component mixed cell line test data",
      "object": "test.data.3comp",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "batch_correction",
      "title": "batch_correction",
      "topics": [
        "batch_correction"
      ]
    },
    {
      "page": "DeMixNB",
      "title": "Deconvolution of heterogeneous tumor samples with two components using expression data from RNAseq or microarray platforms",
      "topics": [
        "DeMixNB"
      ]
    },
    {
      "page": "DeMixNB_preprocessing",
      "title": "DeMixNB_preprocessing",
      "topics": [
        "DeMixNB_preprocessing"
      ]
    },
    {
      "page": "DeMixT",
      "title": "Deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms",
      "topics": [
        "DeMixT"
      ]
    },
    {
      "page": "DeMixT_DE",
      "title": "Estimates the proportions of mixed samples for each mixing component",
      "topics": [
        "DeMixT_DE"
      ]
    },
    {
      "page": "DeMixT_GS",
      "title": "Estimates the proportions of mixed samples for each mixing component using profile likelihood gene selection",
      "topics": [
        "DeMixT_GS"
      ]
    },
    {
      "page": "DeMixT_preprocessing",
      "title": "DeMixT_preprocessing",
      "topics": [
        "DeMixT_preprocessing"
      ]
    },
    {
      "page": "DeMixT_S2",
      "title": "Deconvolves expressions of each individual sample for unknown component",
      "topics": [
        "DeMixT_S2"
      ]
    },
    {
      "page": "detect_suspicious_sample_by_hierarchical_clustering_2comp",
      "title": "detect_suspicious_sample_by_hierarchical_clustering_2comp",
      "topics": [
        "detect_suspicious_sample_by_hierarchical_clustering_2comp",
        "plot_sd"
      ]
    },
    {
      "page": "gene_selection_DE",
      "title": "gene_selection_DE",
      "topics": [
        "gene_selection_DE"
      ]
    },
    {
      "page": "Optimum_KernelC",
      "title": "Kernel function for optimizing parameters and hidden variables in DeMixT",
      "topics": [
        "Optimum_KernelC"
      ]
    },
    {
      "page": "plot_dim",
      "title": "plot_dim",
      "topics": [
        "plot_dim"
      ]
    },
    {
      "page": "scale_normalization_75th_percentile",
      "title": "scale_normalization_75th_percentile",
      "topics": [
        "scale_normalization_75th_percentile"
      ]
    },
    {
      "page": "simulate_2comp",
      "title": "Function to simulate two-component test data",
      "topics": [
        "simulate_2comp"
      ]
    },
    {
      "page": "simulate_3comp",
      "title": "Function to simulate three-component mixed cell line test data",
      "topics": [
        "simulate_3comp"
      ]
    },
    {
      "page": "subset_sd",
      "title": "subset_sd",
      "topics": [
        "subset_sd"
      ]
    },
    {
      "page": "subset_sd_gene_remaining",
      "title": "subset_sd_gene_remaining",
      "topics": [
        "subset_sd_gene_remaining"
      ]
    },
    {
      "page": "test.data.2comp",
      "title": "Simulated two-component test data",
      "topics": [
        "test.data.2comp"
      ]
    },
    {
      "page": "test.data.3comp",
      "title": "Simulated three-component mixed cell line test data",
      "topics": [
        "test.data.3comp"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DeMixT/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "dendextend",
    "edgeR",
    "evd",
    "farver",
    "fastmap",
    "fitdistrplus",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "GPArotation",
    "gridExtra",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixcalc",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "mnormt",
    "nlme",
    "openssl",
    "pbapply",
    "pkgconfig",
    "png",
    "psych",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "statmod",
    "SummarizedExperiment",
    "survival",
    "sva",
    "sys",
    "truncdist",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "XML",
    "xtable",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "DeMixT_tutorial.Rmd",
      "filename": "DeMixT_tutorial.html",
      "title": "A Vignette for DeMixT",
      "author": "Zeya Wang and Fan Gao",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Feature Description",
        "Installation",
        "Functions",
        "Methods",
        "Model",
        "The DeMixT algorithm for deconvolution",
        "Examples",
        "Simulated two-component data",
        "Simulated three-component data",
        "Real data: PRAD in TCGA dataset",
        "Obtain raw read counts for the tumor and normal RNAseq data",
        "Data preprocessing",
        "Deconvolution using DeMixT",
        "Deconvolution using normal reference samples from GTEx",
        "Reference",
        "Session Info"
      ],
      "created": "2026-03-26 21:16:39",
      "modified": "2026-03-26 21:16:39",
      "commits": 1
    },
    {
      "source": "DeMixNB_tutorial.Rmd",
      "filename": "DeMixNB_tutorial.html",
      "title": "DeMixNB: Deconvolution for Sparse Count Data",
      "author": "",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Feature Description",
        "Functions",
        "Methods",
        "Model",
        "The DeMixNB Algorithm for Deconvolution",
        "Real data Example",
        "Spatially Resolved Transcriptomics",
        "Results",
        "Session Information"
      ],
      "created": "2026-03-26 21:16:39",
      "modified": "2026-03-26 21:16:39",
      "commits": 1
    }
  ],
  "_score": 5.778151250383644,
  "_indexed": true,
  "_nocasepkg": "demixt",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-05-28T06:23:21.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "7714007ed87744364a0fb67c31cbd5c8eae7356265e85c7de7b218e3e46732cd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-05-28T06:24:21.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "53abba20ab46d0e729b0fe278dbbe4bca3ea9c27ca405440f7528c0e1e50ddbe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-05-28T06:23:15.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "039ef92ed240b781b87c963625d5fce64530eb8799c8d46091fa9c5cc0b9311b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-05-28T06:23:48.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "7ddb1e7544f3124cd4ce63c6f43d90bb5c18ebf4c4d6d149d851bc0b7160b5ca",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-05-28T06:23:11.000Z",
      "arch": "aarch64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "05920de0e4dad25142c08b6d3772adc4d7da281239063fefb8f3e7b40dff1eab",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-05-28T06:24:50.000Z",
      "arch": "x86_64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "4f60e7f66dabdf886cb10b134e05375df327ac47991fa26a27c4afabe5af2c77",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-05-28T06:23:22.000Z",
      "arch": "aarch64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "6bce01ed199f413ac8babfbcb5cb6c3238c29efaca5a57a39868882964fcf632",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-05-28T06:24:20.000Z",
      "arch": "x86_64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "f4fc1b6f91c2c165b74f2a84c0d41647bc85a8c4ebb76dc431b20784f0e74507",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1.0",
      "date": "2026-05-28T06:23:44.000Z",
      "arch": "emscripten",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "8b7cc1da42bbb245bb16ecbe943fb02f4091860dc8a945a5fe64f5f941bcce79",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-05-28T06:22:17.000Z",
      "arch": "x86_64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "bdf03cb9056547294f9e66423b7efe7e8b3d63a727b025d4da53e539088d3b65",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-05-28T06:22:12.000Z",
      "arch": "x86_64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "5e78be1fc4634187708adaca51c2162d12162fef94b440a5243564b886afbe3b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-05-28T06:23:08.000Z",
      "arch": "x86_64",
      "commit": "7874c43e7a22a104026e39df894e2d52f92971ba",
      "fileid": "e635e9862cf9a1d6c89adf842e20041bcdd22f3c13b719b9f23597c22777c01a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558191924"
    }
  ]
}