{
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  "Package": "BioQC",
  "Type": "Package",
  "Title": "Detect tissue heterogeneity in expression profiles with gene\nsets",
  "Version": "1.41.0",
  "Date": "2021-08-18",
  "Authors@R": "c(\nperson(\"Jitao David\", \"Zhang\", email=\"jitao_david.zhang@roche.com\", role = c(\"cre\", \"aut\")),\nperson(\"Laura\", \"Badi\", role=\"aut\"),\nperson(\"Gregor\", \"Sturm\", email=\"mail@gregor-sturm.de\", role=c(\"aut\")),\nperson(\"Roland\", \"Ambs\", role=\"aut\"),\nperson(\"Iakov\", \"Davydov\", role=\"aut\"))",
  "Description": "BioQC performs quality control of high-throughput\nexpression data based on tissue gene signatures. It can detect\ntissue heterogeneity in gene expression data. The core\nalgorithm is a Wilcoxon-Mann-Whitney test that is optimised for\nhigh performance.",
  "biocViews": "GeneExpression,QualityControl,StatisticalMethod,\nGeneSetEnrichment",
  "Collate": "AllClasses.R AllMethods.R as.GmtList.R GmtList-funcs.R\nreadSignedGmt.R uniqGenesetsByNamespace.R appendGmtList.R\nutils.R entropy.R gini.R readGmt.R matchGenes.R wmwTest.R\nreadCurrentSignatures.R prettySigNames.R leadingEdge.R",
  "VignetteBuilder": "knitr",
  "License": "GPL (>=3) + file LICENSE",
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  "URL": "https://accio.github.io/BioQC",
  "BugReports": "https://accio.github.io/BioQC/issues",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:16 UTC",
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  "Author": "Jitao David Zhang [cre, aut],\nLaura Badi [aut],\nGregor Sturm [aut],\nRoland Ambs [aut],\nIakov Davydov [aut]",
  "Maintainer": "Jitao David Zhang <jitao_david.zhang@roche.com>",
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    "appendGmtList",
    "as.GmtList",
    "entropy",
    "entropyDiversity",
    "entropySpecificity",
    "filterBySize",
    "filterPmat",
    "getLeadingEdgeIndexFromMatrix",
    "getLeadingEdgeIndexFromVector",
    "gini",
    "GmtList",
    "gmtlist2signedGenesets",
    "gsDesc",
    "gsGeneCount",
    "gsGenes",
    "gsName",
    "gsNamespace",
    "gsNamespace<-",
    "gsSize",
    "hasNamespace",
    "IndexList",
    "isValidBaseIndexList",
    "isValidGmtList",
    "isValidIndexList",
    "isValidSignedGenesets",
    "isValidSignedIndexList",
    "matchGenes",
    "offset",
    "offset<-",
    "prettySigNames",
    "readCurrentSignatures",
    "readGmt",
    "readSignedGmt",
    "sampleSpecialization",
    "setDescAsNamespace",
    "setNamespace",
    "show",
    "SignedGenesets",
    "SignedIndexList",
    "simplifyMatrix",
    "uniqGenesetsByNamespace",
    "wmwLeadingEdge",
    "wmwTest",
    "wmwTestInR"
  ],
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      "page": "sub-.GmtList",
      "title": "Subsetting GmtList object into another GmtList object",
      "topics": [
        "[.GmtList"
      ]
    },
    {
      "page": "sub-sub-.GmtList",
      "title": "Subsetting GmtList object to fetch one gene-set",
      "topics": [
        "[[.GmtList"
      ]
    },
    {
      "page": "absLog10p",
      "title": "Absolute base-10 logarithm of p-values",
      "topics": [
        "absLog10p"
      ]
    },
    {
      "page": "appendGmtList",
      "title": "Append a GmtList object to another one",
      "topics": [
        "appendGmtList"
      ]
    },
    {
      "page": "as.GmtList",
      "title": "Convert a list of gene symbols into a gmtlist",
      "topics": [
        "as.GmtList"
      ]
    },
    {
      "page": "BaseIndexList-class",
      "title": "An S4 class to hold a list of indices, with the possibility to specify the offset of the indices. IndexList and SignedIndexList extend this class",
      "topics": [
        "BaseIndexList-class"
      ]
    },
    {
      "page": "entropy",
      "title": "Shannon entropy",
      "topics": [
        "entropy"
      ]
    },
    {
      "page": "entropyDiversity",
      "title": "Entropy-based sample diversity",
      "topics": [
        "entropyDiversity"
      ]
    },
    {
      "page": "entropySpecificity",
      "title": "Entropy-based gene-expression specificity",
      "topics": [
        "entropySpecificity"
      ]
    },
    {
      "page": "filterBySize",
      "title": "Filter a GmtList by size",
      "topics": [
        "filterBySize"
      ]
    },
    {
      "page": "filterPmat",
      "title": "Filter rows of p-value matrix under the significance threshold",
      "topics": [
        "filterPmat"
      ]
    },
    {
      "page": "getLeadingEdgeIndexFromVector",
      "title": "Getting leading-edge indices from a vector",
      "topics": [
        "getLeadingEdgeIndexFromMatrix",
        "getLeadingEdgeIndexFromVector"
      ]
    },
    {
      "page": "gini",
      "title": "Calculate Gini Index of a numeric vector",
      "topics": [
        "gini"
      ]
    },
    {
      "page": "GmtList",
      "title": "Convert a list to a GmtList object",
      "topics": [
        "GmtList"
      ]
    },
    {
      "page": "GmtList-class",
      "title": "An S4 class to hold geneset in the GMT file in a list, each item in the list is in in turn a list containing following items: name, desc, and genes.",
      "topics": [
        "GmtList-class"
      ]
    },
    {
      "page": "gmtlist2signedGenesets",
      "title": "Convert gmtlist into a list of signed genesets",
      "topics": [
        "gmtlist2signedGenesets"
      ]
    },
    {
      "page": "gsDesc",
      "title": "Gene-set descriptions",
      "topics": [
        "gsDesc"
      ]
    },
    {
      "page": "gsGeneCount",
      "title": "Gene-set gene counts",
      "topics": [
        "gsGeneCount",
        "gsSize"
      ]
    },
    {
      "page": "gsGenes",
      "title": "Gene-set member genes",
      "topics": [
        "gsGenes"
      ]
    },
    {
      "page": "gsName",
      "title": "Gene-set names",
      "topics": [
        "gsName"
      ]
    },
    {
      "page": "gsNamespace",
      "title": "Gene-set namespaces",
      "topics": [
        "gsNamespace"
      ]
    },
    {
      "page": "setGsNamespace",
      "title": "gsNamespace<- is the synonym of setGsNamespace",
      "topics": [
        "gsNamespace<-"
      ]
    },
    {
      "page": "hasNamespace",
      "title": "Whether namespace is set",
      "topics": [
        "hasNamespace"
      ]
    },
    {
      "page": "IndexList",
      "title": "Convert a list to an IndexList object",
      "topics": [
        "IndexList",
        "IndexList,list-method",
        "IndexList,logical-method",
        "IndexList,numeric-method"
      ]
    },
    {
      "page": "IndexList-class",
      "title": "An S4 class to hold a list of integers as indices, with the possibility to specify the offset of the indices",
      "topics": [
        "IndexList-class"
      ]
    },
    {
      "page": "isValidBaseIndexList",
      "title": "Function to validate a BaseIndexList object",
      "topics": [
        "isValidBaseIndexList"
      ]
    },
    {
      "page": "isValidGmtList",
      "title": "Function to validate a GmtList object",
      "topics": [
        "isValidGmtList"
      ]
    },
    {
      "page": "isValidIndexList",
      "title": "Function to validate an IndexList object",
      "topics": [
        "isValidIndexList"
      ]
    },
    {
      "page": "isValidSignedGenesets",
      "title": "Function to validate a SignedGenesets object",
      "topics": [
        "isValidSignedGenesets"
      ]
    },
    {
      "page": "isValidSignedIndexList",
      "title": "Function to validate a SignedIndexList object",
      "topics": [
        "isValidSignedIndexList"
      ]
    },
    {
      "page": "matchGenes",
      "title": "Match genes in a list-like object to a vector of genesymbols",
      "topics": [
        "matchGenes",
        "matchGenes,character,character-method",
        "matchGenes,character,DGEList-method",
        "matchGenes,character,eSet-method",
        "matchGenes,character,matrix-method",
        "matchGenes,GmtList,character-method",
        "matchGenes,GmtList,DGEList-method",
        "matchGenes,GmtList,eSet-method",
        "matchGenes,GmtList,matrix-method",
        "matchGenes,SignedGenesets,character-method",
        "matchGenes,SignedGenesets,DGEList-method",
        "matchGenes,SignedGenesets,eSet-method",
        "matchGenes,SignedGenesets,matrix-method"
      ]
    },
    {
      "page": "offset",
      "title": "Get offset from an IndexList object",
      "topics": [
        "offset",
        "offset,BaseIndexList-method"
      ]
    },
    {
      "page": "offset-set",
      "title": "Set the offset of an 'IndexList' or a 'SignedIndexList' object",
      "topics": [
        "offset-set",
        "offset<-",
        "offset<-,IndexList,numeric-method",
        "offset<-,SignedIndexList,numeric-method"
      ]
    },
    {
      "page": "prettySigNames",
      "title": "Prettify default signature names",
      "topics": [
        "prettySigNames"
      ]
    },
    {
      "page": "readCurrentSignatures",
      "title": "Load current BioQC signatures",
      "topics": [
        "readCurrentSignatures"
      ]
    },
    {
      "page": "readGmt",
      "title": "Read in gene-sets from a GMT file",
      "topics": [
        "readGmt"
      ]
    },
    {
      "page": "readSignedGmt",
      "title": "Read signed GMT files",
      "topics": [
        "readSignedGmt"
      ]
    },
    {
      "page": "sampleSpecialization",
      "title": "Entropy-based sample specialization",
      "topics": [
        "sampleSpecialization"
      ]
    },
    {
      "page": "setDescAsNamespace",
      "title": "Set gene-set description as namespace",
      "topics": [
        "setDescAsNamespace"
      ]
    },
    {
      "page": "setNamespace",
      "title": "Set the namespace field in each gene-set within a GmtList",
      "topics": [
        "setNamespace"
      ]
    },
    {
      "page": "show-GmtList-method",
      "title": "Show method for GmtList",
      "topics": [
        "show,GmtList-method"
      ]
    },
    {
      "page": "show-IndexList-method",
      "title": "Show method for IndexList",
      "topics": [
        "show,IndexList-method"
      ]
    },
    {
      "page": "show-SignedGenesets-method",
      "title": "Show method for SignedGenesets",
      "topics": [
        "show,SignedGenesets-method"
      ]
    },
    {
      "page": "show-SignedIndexList-method",
      "title": "Show method for SignedIndexList",
      "topics": [
        "show,SignedIndexList-method"
      ]
    },
    {
      "page": "SignedGenesets",
      "title": "Convert a list to a SignedGenesets object",
      "topics": [
        "SignedGenesets"
      ]
    },
    {
      "page": "SignedGenesets-class",
      "title": "An S4 class to hold signed genesets, each item in the list is in in turn a list containing following items: name, pos, and neg.",
      "topics": [
        "SignedGenesets-class"
      ]
    },
    {
      "page": "SignedIndexList",
      "title": "Convert a list into a SignedIndexList",
      "topics": [
        "SignedIndexList",
        "SignedIndexList,list-method"
      ]
    },
    {
      "page": "SignedIndexList-class",
      "title": "An S4 class to hold a list of signed integers as indices, with the possibility to specify the offset of the indices",
      "topics": [
        "SignedIndexList-class"
      ]
    },
    {
      "page": "simplifyMatrix",
      "title": "Simplify matrix in case of single row/columns",
      "topics": [
        "simplifyMatrix"
      ]
    },
    {
      "page": "uniqGenesetsByNamespace",
      "title": "Make names of gene-sets unique by namespace, and member genes of gene-sets unique",
      "topics": [
        "uniqGenesetsByNamespace"
      ]
    },
    {
      "page": "valTypes",
      "title": "prints the options of valTypes of wmwTest",
      "topics": [
        "valTypes"
      ]
    },
    {
      "page": "wmwLeadingEdge",
      "title": "Identify BioQC leading-edge genes of one gene-set",
      "topics": [
        "wmwLeadingEdge"
      ]
    },
    {
      "page": "wmwTest",
      "title": "Wilcoxon-Mann-Whitney rank sum test for high-throughput expression profiling data",
      "topics": [
        "wmwTest",
        "wmwTest,ANY,list-method",
        "wmwTest,ANY,logical-method",
        "wmwTest,ANY,numeric-method",
        "wmwTest,eSet,GmtList-method",
        "wmwTest,eSet,list-method",
        "wmwTest,eSet,logical-method",
        "wmwTest,eSet,numeric-method",
        "wmwTest,eSet,SignedGenesets-method",
        "wmwTest,eSet,SignedIndexList-method",
        "wmwTest,matrix,GmtList-method",
        "wmwTest,matrix,IndexList-method",
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