BioassayDB-class        Class '"BioassayDB"'
activeAgainst           Show compounds active against a specified
                        target
activeTargets           Show targets against which a small molecule is
                        active
addBioassayIndex        Index a bioassayR database
addDataSource           Add a new data source to a bioassayR database
allCids                 List compound cids in a 'BioassayDB',
                        'bioassay', 'bioassaySet', or target matrix
                        ('dgCMatrix') object
allTargets              List distinct target(s) in a 'BioassayDB',
                        'bioassay', 'bioassaySet', or target matrix
                        ('dgCMatrix') object
assaySetTargets         Return targets of assays in a 'bioassaySet'
                        object
bioactivityFingerprint
                        Create an 'ChemmineR' 'FPset' object that
                        contains bioactivity results for a given set of
                        compounds and targets.
bioassay-class          Class '"bioassay"'
bioassaySet-class       Class '"bioassaySet"'
connectBioassayDB       Create a 'BioassayDB' object connected to the
                        specified database file
crossReactivityProbability
                        Compute the probability that compounds in a
                        compound vs target matrix are promiscuous
                        binders
disconnectBioassayDB    Disconnect the database file from a
                        'BioassayDB' object
dropBioassay            Delete an assay from a bioassayR database
dropBioassayIndex       Remove index from a bioassayR database
getAssay                Retrieve a bioassay
getAssays               Retrieve multiple bioassays from a database
getBioassaySetByCids    Create 'bioassaySet' sparse matrix object with
                        activity data only for specified compounds
inactiveTargets         Takes a single cid and returns a table of the
                        proteins it has been found inactive against.
loadBioassay            Add an assay to the database
loadIdMapping           Load a target identifier mapping into a
                        bioassayR database
newBioassayDB           Create a new bioassayR database
parsePubChemBioassay    Parse PubChem Bioassay Data
perTargetMatrix         Collapse a 'bioassaySet' object from multiple
                        assays by combining assays with a common target
queryBioassayDB         Perform a SQL query on a bioassayR database
samplebioassay          Sample activity data for use with bioassayR
scaleBioassaySet        Centers and standardizes the numeric activity
                        scores for a 'bioassaySet' object (creates
                        Z-scores)
screenedAtLeast         Return all compounds in the database screened
                        at least 'minTargets' times.
selectiveAgainst        Identify small molecules with selective binding
                        against a target of interest
targetSelectivity       Returns the target selectivity for a specified
                        list of compounds (cids).
translateTargetId       Translate a protein target identifier to
                        another identifier system
trinarySimilarity       Computes the tanimoto similarity coefficient
                        between the bioactivity profiles of two
                        compounds, each represented as a column in a
                        compound vs. target sparse matrix
