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  "Title": "Cross-target analysis of small molecule bioactivity",
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  "Date": "2024-10-21",
  "Author": "Tyler Backman, Ronly Schlenk, Thomas Girke",
  "Maintainer": "Thomas Girke <tgirke@citrus.ucr.edu>",
  "Description": "bioassayR is a computational tool that enables\nsimultaneous analysis of thousands of bioassay experiments\nperformed over a diverse set of compounds and biological\ntargets. Unique features include support for large-scale\ncross-target analyses of both public and custom bioassays,\ngeneration of high throughput screening fingerprints (HTSFPs),\nand an optional preloaded database that provides access to a\nsubstantial portion of publicly available bioactivity data.",
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    "activeTargets",
    "activity",
    "activity<-",
    "addBioassayIndex",
    "addDataSource",
    "aid",
    "aid<-",
    "allCids",
    "allTargets",
    "assay_type",
    "assay_type<-",
    "assaySetTargets",
    "bioactivityFingerprint",
    "connectBioassayDB",
    "crossReactivityPrior",
    "crossReactivityProbability",
    "disconnectBioassayDB",
    "dropBioassay",
    "dropBioassayIndex",
    "getAssay",
    "getAssays",
    "getBioassaySetByCids",
    "inactiveTargets",
    "loadBioassay",
    "loadIdMapping",
    "newBioassayDB",
    "organism",
    "organism<-",
    "parsePubChemBioassay",
    "perTargetMatrix",
    "queryBioassayDB",
    "scaleBioassaySet",
    "scores",
    "scores<-",
    "scoring",
    "scoring<-",
    "screenedAtLeast",
    "selectiveAgainst",
    "show",
    "source_id",
    "source_id<-",
    "sources",
    "sources<-",
    "target_types",
    "target_types<-",
    "targets",
    "targets<-",
    "targetSelectivity",
    "translateTargetId",
    "trinarySimilarity"
  ],
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    {
      "name": "samplebioassay",
      "title": "Sample activity data for use with bioassayR",
      "object": "samplebioassay",
      "file": "samplebioassay.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "cid",
        "activity",
        "score"
      ],
      "rows": 57,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "activeAgainst",
      "title": "Show compounds active against a specified target",
      "topics": [
        "activeAgainst"
      ]
    },
    {
      "page": "activeTargets",
      "title": "Show targets against which a small molecule is active",
      "topics": [
        "activeTargets"
      ]
    },
    {
      "page": "addBioassayIndex",
      "title": "Index a bioassayR database",
      "topics": [
        "addBioassayIndex"
      ]
    },
    {
      "page": "addDataSource",
      "title": "Add a new data source to a bioassayR database",
      "topics": [
        "addDataSource"
      ]
    },
    {
      "page": "allCids",
      "title": "List compound cids in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') object",
      "topics": [
        "allCids"
      ]
    },
    {
      "page": "allTargets",
      "title": "List distinct target(s) in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') object",
      "topics": [
        "allTargets"
      ]
    },
    {
      "page": "assaySetTargets",
      "title": "Return targets of assays in a 'bioassaySet' object",
      "topics": [
        "assaySetTargets"
      ]
    },
    {
      "page": "bioactivityFingerprint",
      "title": "Create an 'ChemmineR' 'FPset' object that contains bioactivity results for a given set of compounds and targets.",
      "topics": [
        "bioactivityFingerprint"
      ]
    },
    {
      "page": "bioassay-class",
      "title": "Class '\"bioassay\"'",
      "topics": [
        "aid",
        "aid,bioassay-method",
        "aid<-",
        "aid<-,bioassay-method",
        "assay_type",
        "assay_type,bioassay-method",
        "assay_type<-",
        "assay_type<-,bioassay-method",
        "bioassay",
        "bioassay-class",
        "organism",
        "organism,bioassay-method",
        "organism<-",
        "organism<-,bioassay-method",
        "scores",
        "scores,bioassay-method",
        "scores<-",
        "scores<-,bioassay-method",
        "scoring",
        "scoring,bioassay-method",
        "scoring<-",
        "scoring<-,bioassay-method",
        "show",
        "show,bioassay-method",
        "source_id",
        "source_id,bioassay-method",
        "source_id<-",
        "source_id<-,bioassay-method",
        "targets",
        "targets,bioassay-method",
        "targets<-",
        "targets<-,bioassay-method",
        "target_types",
        "target_types,bioassay-method",
        "target_types<-",
        "target_types<-,bioassay-method"
      ]
    },
    {
      "page": "BioAssayDB-class",
      "title": "Class '\"BioassayDB\"'",
      "topics": [
        "BioassayDB-class",
        "queryBioassayDB,BioassayDB-method",
        "show,BioassayDB-method"
      ]
    },
    {
      "page": "bioassaySet-class",
      "title": "Class '\"bioassaySet\"'",
      "topics": [
        "activity",
        "activity,bioassaySet-method",
        "activity<-",
        "activity<-,bioassaySet-method",
        "assay_type,bioassaySet-method",
        "assay_type<-,bioassaySet-method",
        "bioassaySet-class",
        "organism,bioassaySet-method",
        "organism<-,bioassaySet-method",
        "scores,bioassaySet-method",
        "scores<-,bioassaySet-method",
        "scoring,bioassaySet-method",
        "scoring<-,bioassaySet-method",
        "show,bioassaySet-method",
        "sources",
        "sources,bioassaySet-method",
        "sources<-",
        "sources<-,bioassaySet-method",
        "source_id,bioassaySet-method",
        "source_id<-,bioassaySet-method",
        "targets,bioassaySet-method",
        "targets<-,bioassaySet-method",
        "target_types,bioassaySet-method",
        "target_types<-,bioassaySet-method"
      ]
    },
    {
      "page": "connectBioassayDB",
      "title": "Create a 'BioassayDB' object connected to the specified database file",
      "topics": [
        "connectBioassayDB"
      ]
    },
    {
      "page": "crossReactivityProbability",
      "title": "Compute the probability that compounds in a compound vs target matrix are promiscuous binders",
      "topics": [
        "crossReactivityPrior",
        "crossReactivityProbability"
      ]
    },
    {
      "page": "disconnectBioassayDB",
      "title": "Disconnect the database file from a 'BioassayDB' object",
      "topics": [
        "disconnectBioassayDB"
      ]
    },
    {
      "page": "dropBioassay",
      "title": "Delete an assay from a bioassayR database",
      "topics": [
        "dropBioassay"
      ]
    },
    {
      "page": "dropBioassayIndex",
      "title": "Remove index from a bioassayR database",
      "topics": [
        "dropBioassayIndex"
      ]
    },
    {
      "page": "getAssay",
      "title": "Retrieve a bioassay",
      "topics": [
        "getAssay"
      ]
    },
    {
      "page": "getAssays",
      "title": "Retrieve multiple bioassays from a database",
      "topics": [
        "getAssays"
      ]
    },
    {
      "page": "getBioassaySetByCids",
      "title": "Create 'bioassaySet' sparse matrix object with activity data only for specified compounds",
      "topics": [
        "getBioassaySetByCids"
      ]
    },
    {
      "page": "inactiveTargets",
      "title": "Takes a single cid and returns a table of the proteins it has been found inactive against.",
      "topics": [
        "inactiveTargets"
      ]
    },
    {
      "page": "loadBioassay",
      "title": "Add an assay to the database",
      "topics": [
        "loadBioassay"
      ]
    },
    {
      "page": "loadIdMapping",
      "title": "Load a target identifier mapping into a bioassayR database",
      "topics": [
        "loadIdMapping"
      ]
    },
    {
      "page": "newBioassayDB",
      "title": "Create a new bioassayR database",
      "topics": [
        "newBioassayDB"
      ]
    },
    {
      "page": "parsePubChemBioassay",
      "title": "Parse PubChem Bioassay Data",
      "topics": [
        "parsePubChemBioassay"
      ]
    },
    {
      "page": "perTargetMatrix",
      "title": "Collapse a 'bioassaySet' object from multiple assays by combining assays with a common target",
      "topics": [
        "perTargetMatrix"
      ]
    },
    {
      "page": "queryBioassayDB",
      "title": "Perform a SQL query on a bioassayR database",
      "topics": [
        "queryBioassayDB"
      ]
    },
    {
      "page": "samplebioassay",
      "title": "Sample activity data for use with bioassayR",
      "topics": [
        "samplebioassay"
      ]
    },
    {
      "page": "scaleBioassaySet",
      "title": "Centers and standardizes the numeric activity scores for a 'bioassaySet' object (creates Z-scores)",
      "topics": [
        "scaleBioassaySet"
      ]
    },
    {
      "page": "screenedAtLeast",
      "title": "Return all compounds in the database screened at least 'minTargets' times.",
      "topics": [
        "screenedAtLeast"
      ]
    },
    {
      "page": "selectiveAgainst",
      "title": "Identify small molecules with selective binding against a target of interest",
      "topics": [
        "selectiveAgainst"
      ]
    },
    {
      "page": "targetSelectivity",
      "title": "Returns the target selectivity for a specified list of compounds (cids).",
      "topics": [
        "targetSelectivity"
      ]
    },
    {
      "page": "translateTargetId",
      "title": "Translate a protein target identifier to another identifier system",
      "topics": [
        "translateTargetId"
      ]
    },
    {
      "page": "trinarySimilarity",
      "title": "Computes the tanimoto similarity coefficient between the bioactivity profiles of two compounds, each represented as a column in a compound vs. target sparse matrix",
      "topics": [
        "trinarySimilarity"
      ]
    }
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      "title": "bioassayR Introduction and Examples",
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      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting Started",
        "Installation",
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        "Quick Tutorial",
        "Examples",
        "Loading User Supplied PubChem BioAssay Data",
        "Prebuilt Database Example: Investigate Activity of a Known Drug",
        "Identify Target Selective Compounds",
        "Cluster Compounds by Activity Profile",
        "Analyze and Load Raw Screening Data",
        "Custom SQL Queries",
        "Building PubChem BioAssay Database",
        "Version Information",
        "Funding",
        "References"
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      "created": "2015-10-07 17:52:54",
      "modified": "2024-10-22 04:08:22",
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