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  "_id": "6a1bcf181d7bb097a0a13fbd",
  "Package": "ccfindR",
  "Version": "1.33.0",
  "Date": "2019-10-1",
  "Title": "Cancer Clone Finder",
  "Authors@R": "c(person('Jun','Woo',role=c('aut','cre'),email='jwoo@umn.edu'),\nperson('Jinhua','Wang',role='aut',email='wangjh@umn.edu'))",
  "RdMacros": "Rdpack",
  "biocViews": "Transcriptomics, SingleCell, ImmunoOncology, Bayesian,\nClustering",
  "Description": "A collection of tools for cancer genomic data clustering\nanalyses, including those for single cell RNA-seq. Cell\nclustering and feature gene selection analysis employ Bayesian\n(and maximum likelihood) non-negative matrix factorization\n(NMF) algorithm. Input data set consists of RNA count matrix,\ngene, and cell bar code annotations.  Analysis outputs are\nfactor matrices for multiple ranks and marginal likelihood\nvalues for each rank. The package includes utilities for\ndownstream analyses, including meta-gene identification,\nvisualization, and construction of rank-based trees for\nclusters.",
  "License": "GPL (>= 2)",
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  "URL": "http://dx.doi.org/10.26508/lsa.201900443",
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  "Author": "Jun Woo [aut, cre], Jinhua Wang [aut]",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:53 UTC",
  "RemoteUrl": "https://github.com/bioc/ccfindR",
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    "rowData",
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    {
      "page": "subset-methods",
      "title": "Subsetting scNMFSet object",
      "topics": [
        "[,scNMFSet,ANY,ANY,ANY-method",
        "[,scNMFSet-method"
      ]
    },
    {
      "page": "assignCelltype",
      "title": "Cell type assignment via GSEA",
      "topics": [
        "assignCelltype"
      ]
    },
    {
      "page": "basis",
      "title": "Basis matrices in an Object",
      "topics": [
        "basis"
      ]
    },
    {
      "page": "basis-scNMFSet-method",
      "title": "Basis matrix accessor",
      "topics": [
        "basis,scNMFSet-method"
      ]
    },
    {
      "page": "basis-set",
      "title": "Generics for basis matrix assignment",
      "topics": [
        "basis<-"
      ]
    },
    {
      "page": "basis-set-scNMFSet-method",
      "title": "Modify basis matrices",
      "topics": [
        "basis<-,scNMFSet-method"
      ]
    },
    {
      "page": "build_tree",
      "title": "Build tree connecting clusters at different ranks",
      "topics": [
        "build_tree"
      ]
    },
    {
      "page": "ccfindR",
      "title": "ccfindR: Cancer Clone FindeR",
      "topics": [
        "ccfindR-package",
        "ccfindR"
      ]
    },
    {
      "page": "cell_map",
      "title": "Plot heatmap of clustering coefficient matrix",
      "topics": [
        "cell_map"
      ]
    },
    {
      "page": "cluster_id",
      "title": "Assign cells into clusters",
      "topics": [
        "cluster_id"
      ]
    },
    {
      "page": "coeff",
      "title": "Coefficient matrices in an Object",
      "topics": [
        "coeff"
      ]
    },
    {
      "page": "coeff-scNMFSet-method",
      "title": "Coefficient matrix accessor",
      "topics": [
        "coeff,scNMFSet-method"
      ]
    },
    {
      "page": "coeff-set",
      "title": "Generics for coefficient matrix assignment",
      "topics": [
        "coeff<-"
      ]
    },
    {
      "page": "coeff-set-scNMFSet-method",
      "title": "Modify coefficient matrices",
      "topics": [
        "coeff<-,scNMFSet-method"
      ]
    },
    {
      "page": "colData-scNMFSet-method",
      "title": "Sample annotation accessor",
      "topics": [
        "colData,scNMFSet-method"
      ]
    },
    {
      "page": "colData-set-scNMFSet-ANY-method",
      "title": "Cell annotation assignment",
      "topics": [
        "colData<-,scNMFSet,ANY-method"
      ]
    },
    {
      "page": "counts-scNMFSet-method",
      "title": "Accessor for count matrix",
      "topics": [
        "counts,scNMFSet-method"
      ]
    },
    {
      "page": "counts-set-scNMFSet-method",
      "title": "Assignment of count matrix",
      "topics": [
        "counts<-,scNMFSet-method"
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    },
    {
      "page": "dbasis",
      "title": "Basis SD matrix accessor",
      "topics": [
        "dbasis"
      ]
    },
    {
      "page": "dbasis-scNMFSet-method",
      "title": "Basis SD matrix accessor",
      "topics": [
        "dbasis,scNMFSet-method"
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    },
    {
      "page": "dbasis-set",
      "title": "Basis SD matrix assignment",
      "topics": [
        "dbasis<-"
      ]
    },
    {
      "page": "dbasis-set-scNMFSet-method",
      "title": "Modify dbasis matrices",
      "topics": [
        "dbasis<-,scNMFSet-method"
      ]
    },
    {
      "page": "dcoeff",
      "title": "Coeff SD matrix accessor",
      "topics": [
        "dcoeff"
      ]
    },
    {
      "page": "dcoeff-scNMFSet-method",
      "title": "Coeffcient SD matrix accessor",
      "topics": [
        "dcoeff,scNMFSet-method"
      ]
    },
    {
      "page": "dcoeff-set",
      "title": "Coeff SD matrix assignment",
      "topics": [
        "dcoeff<-"
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    },
    {
      "page": "dcoeff-set-scNMFSet-method",
      "title": "Modify dcoeff matrices",
      "topics": [
        "dcoeff<-,scNMFSet-method"
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    },
    {
      "page": "factorize",
      "title": "Maximum likelihood factorization",
      "topics": [
        "factorize"
      ]
    },
    {
      "page": "feature_map",
      "title": "Plot heatmap of basis matrix",
      "topics": [
        "feature_map"
      ]
    },
    {
      "page": "filter_cells",
      "title": "Filter cells with quality control criteria",
      "topics": [
        "filter_cells"
      ]
    },
    {
      "page": "filter_genes",
      "title": "Filter genes with quality control criteria",
      "topics": [
        "filter_genes"
      ]
    },
    {
      "page": "gene_map",
      "title": "Plot heatmap of metagene matrix",
      "topics": [
        "gene_map"
      ]
    },
    {
      "page": "measure",
      "title": "Factorization measures in an Object",
      "topics": [
        "measure"
      ]
    },
    {
      "page": "measure-scNMFSet-method",
      "title": "Rank measure accessor",
      "topics": [
        "measure,scNMFSet-method"
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    },
    {
      "page": "measure-set",
      "title": "Generics for factorization measure assignment",
      "topics": [
        "measure<-"
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    },
    {
      "page": "measure-set-scNMFSet-method",
      "title": "Modify factorization measure",
      "topics": [
        "measure<-,scNMFSet-method"
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    },
    {
      "page": "meta_gene.cv",
      "title": "Meta gene table with CV",
      "topics": [
        "meta_gene.cv"
      ]
    },
    {
      "page": "meta_genes",
      "title": "Find metagenes from basis matrix",
      "topics": [
        "meta_genes"
      ]
    },
    {
      "page": "newick",
      "title": "Generate Newick format tree string from tree list object",
      "topics": [
        "newick"
      ]
    },
    {
      "page": "normalize_count",
      "title": "Normalize count data",
      "topics": [
        "normalize_count"
      ]
    },
    {
      "page": "optimal_rank",
      "title": "Determine optimal rank",
      "topics": [
        "optimal_rank"
      ]
    },
    {
      "page": "plot_genes",
      "title": "Plot gene variance distributions",
      "topics": [
        "plot_genes"
      ]
    },
    {
      "page": "plot_tree",
      "title": "Plot cluster tree",
      "topics": [
        "plot_tree"
      ]
    },
    {
      "page": "ranks",
      "title": "Rank values in an Object",
      "topics": [
        "ranks"
      ]
    },
    {
      "page": "ranks-scNMFSet-method",
      "title": "Rank accessor",
      "topics": [
        "ranks,scNMFSet-method"
      ]
    },
    {
      "page": "ranks-set",
      "title": "Generics for ranks assignment",
      "topics": [
        "ranks<-"
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    },
    {
      "page": "ranks-set-scNMFSet-method",
      "title": "Modify ranks",
      "topics": [
        "ranks<-,scNMFSet-method"
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    },
    {
      "page": "read_10x",
      "title": "Read 10x data and generate scNMF object",
      "topics": [
        "read_10x"
      ]
    },
    {
      "page": "remove_zeros",
      "title": "Remove rows or columns that are empty from an object",
      "topics": [
        "remove_zeros"
      ]
    },
    {
      "page": "rename_tips",
      "title": "Rename tips of trees with cell types",
      "topics": [
        "rename_tips"
      ]
    },
    {
      "page": "rowData-scNMFSet-method",
      "title": "Feature annotation accessor",
      "topics": [
        "rowData,scNMFSet-method"
      ]
    },
    {
      "page": "rowData-set-scNMFSet-method",
      "title": "Gene annotation assignment",
      "topics": [
        "rowData<-,scNMFSet-method"
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    },
    {
      "page": "scNMFSet",
      "title": "Create 'scNMFSet' object",
      "topics": [
        "scNMFSet"
      ]
    },
    {
      "page": "scNMFSet-class",
      "title": "Class 'scNMFSet' for storing input data and results",
      "topics": [
        "plot,scNMFSet,ANY-method",
        "scNMFSet-class"
      ]
    },
    {
      "page": "show-scNMFSet-method",
      "title": "Display object",
      "topics": [
        "show,scNMFSet-method"
      ]
    },
    {
      "page": "simulate_data",
      "title": "Generate simulated data for factorization",
      "topics": [
        "simulate_data"
      ]
    },
    {
      "page": "simulate_whx",
      "title": "Simulate factor matrices and data using priors",
      "topics": [
        "simulate_whx"
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    },
    {
      "page": "vb_factorize",
      "title": "Bayesian NMF inference of count matrix",
      "topics": [
        "vb_factorize"
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    },
    {
      "page": "visualize_clusters",
      "title": "Visualize clusters",
      "topics": [
        "visualize_clusters"
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    {
      "page": "write_10x",
      "title": "Write 10x data files",
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    {
      "page": "write_meta",
      "title": "Write meta genes to a file",
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      "source": "ccfindR.Rmd",
      "filename": "ccfindR.html",
      "title": "ccfindR: single-cell RNA-seq analysis using Bayesian non-negative matrix factorization",
      "author": "Jun Woo, Constantin Aliferis, Jinhua Wang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Algorithm",
        "Workflow",
        "Installation",
        "Data input",
        "Quality control",
        "Rank determination",
        "Bayesian NMF",
        "Visualization",
        "References"
      ],
      "created": "2018-03-17 09:14:34",
      "modified": "2019-07-08 20:15:01",
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