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  "Version": "1.27.0",
  "Date": "2019-03-09",
  "Title": "A dimensionality reduction tool using gene detection pattern to\nmitigate noisy expression profile of scRNA-seq",
  "Description": "This package is designed to model gene detection pattern\nof scRNA-seq through a binary factor analysis model. This model\nallows user to pass into a cell level covariate matrix X and\ngene level covariate matrix Q to account for nuisance\nvariance(e.g batch effect), and it will output a low\ndimensional embedding matrix for downstream analysis.",
  "Authors@R": "c(person(given = \"Ruoxin\",\nfamily = \"Li\",\nrole = c(\"aut\", \"cre\"),\nemail = \"uskli@ucdavis.edu\"),\nperson(given = \"Gerald\",\nfamily = \"Quon\",\nrole = c(\"aut\"),\nemail = \"gquon@ucdavis.edu\"))",
  "URL": "https://github.com/ucdavis/quon-titative-biology/BFA",
  "BugReports": "https://github.com/ucdavis/quon-titative-biology/BFA/issues",
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  "License": "GPL-3 + file LICENSE",
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  "Config/pak/sysreqs": "cmake libglpk-dev make libgsl0-dev libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:38 UTC",
  "RemoteUrl": "https://github.com/bioc/scBFA",
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    "User": "root"
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  "Author": "Ruoxin Li [aut, cre],\nGerald Quon [aut]",
  "Maintainer": "Ruoxin Li <uskli@ucdavis.edu>",
  "MD5sum": "b5e9954c3f0f811618759ffc8e492ae6",
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    },
    {
      "name": "zinb_toy",
      "title": "example zinb object after fitting a toy dataset with 5 cells and 10 genes",
      "object": "zinb_toy",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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  ],
  "_help": [
    {
      "page": "BinaryPCA",
      "title": "Performs Binary PCA (as outlined in our paper). This function take the input of gene expression profile and perform PCA on gene detection pattern",
      "topics": [
        "BinaryPCA"
      ]
    },
    {
      "page": "celltype",
      "title": "Cell types as labels of example scRNA-seq dataset(exprdata)",
      "topics": [
        "celltype"
      ]
    },
    {
      "page": "celltype_toy",
      "title": "toy cell type vector with 3 cell types generated for 5 cells in toy dataset",
      "topics": [
        "celltype_toy"
      ]
    },
    {
      "page": "diagnose",
      "title": "Perform diagnoisis of dispersion on the expression profile to check whether scBFA works on specific dataset",
      "topics": [
        "diagnose"
      ]
    },
    {
      "page": "disperPlot",
      "title": "Reference dataset(disperPlot)",
      "topics": [
        "disperPlot"
      ]
    },
    {
      "page": "exprdata",
      "title": "scRNA-seq dataset(exprdata)",
      "topics": [
        "exprdata"
      ]
    },
    {
      "page": "getGeneExpr",
      "title": "Function to extract gene expression matrix from input observation matrix",
      "topics": [
        "getGeneExpr"
      ]
    },
    {
      "page": "getLoading",
      "title": "Function to get low dimensional loading matrix",
      "topics": [
        "getLoading"
      ]
    },
    {
      "page": "getScore",
      "title": "Function to get low dimensional embedding matrix",
      "topics": [
        "getScore"
      ]
    },
    {
      "page": "gradient",
      "title": "Calculate gradient of the negative log likelihood, used for calls to the optim() function.",
      "topics": [
        "gradient"
      ]
    },
    {
      "page": "gradient_chunk",
      "title": "Calculate gradient of the negative log likelihood, used for calls to the optim() function.",
      "topics": [
        "gradient_chunk"
      ]
    },
    {
      "page": "scbfa",
      "title": "Perform BFA model on the expression profile",
      "topics": [
        "scBFA"
      ]
    },
    {
      "page": "scNoiseSim",
      "title": "simulation to generate scRNA-seq data with varying level of gene detection noise versus gene count noise",
      "topics": [
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      ]
    },
    {
      "page": "zinb_toy",
      "title": "example zinb object after fitting a toy dataset with 5 cells and 10 genes",
      "topics": [
        "zinb_toy"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/scBFA/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ADGofTest",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "cluster",
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      "title": "Gene Detection Analysis for scRNA-seq",
      "author": "Ruoxin Li, Gerald Quon",
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        "Installation",
        "Information of example dataset",
        "Working with SingleCellExperiment class",
        "Gene Detection Model analysis",
        "Binary Factor Analysis",
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      "modified": "2019-08-07 16:34:40",
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