DrugData                Returns a DrugData object.
DrugData,eSet,eSet,MIAxE-method
                        Returns a DrugData object.
DrugData-class          An S4 class to represent drug activity and
                        related data recorded for a set of biological
                        samples.
Drug_MOA_Key            A data frame with descriptive information for
                        all compound mechanism of action (MOA)
                        abbreviations used in CellMiner.
MolData                 Returns a MolData object.
MolData,list,MIAxE-method
                        Returns a MolData object.
MolData-class           An S4 class to represent molecular data
                        recorded for a set of biological samples.
[[,MolData-method       Returns an indexed eSet object from a MolData
                        object eSet list.
[[<-,MolData-method     Assigns an eSet object to a specified position
                        in a MolData object eSet list.
cmVersion               CellMiner Version
compareFingerprints     Compare Structure Fingerprints to NCI DTP
                        Compounds
crossCors               Calculate cross-correlations with between rows
                        of input matrices
crossCorsSpearman       Calculate Spearman's correlations with between
                        rows of input matrices
drugDB                  CellMiner Drug Response Values
elNetMolDataNCI60       NCI60 Molecular Data
fingerprintList         A list of pre-computed fingerprints using
                        getFingeprintList()
getAct                  Returns an eSet object with drug activity data.
getAct,DrugData-method
                        Returns an eSet object with drug activity data.
getActivityRangeStats   Returns a table of activity range statistics
                        for a set of compounds.
getAllFeatureData       Returns a list of feature data matrices.
getAllFeatureData,MolData-method
                        Returns a list of feature data matrices.
getBinaryMutationData   Compute a binary gene mutation data matrix from
                        SNP and other mutation event-level data.
getColumnQuantiles      Calculate quantile for the columns in a matrix
getDrugActivityData     Returns a matrix containing activity (-logGI50)
                        data for a set of compounds.
getDrugActivityRange    Returns a vector of log activity range values
                        for set of compounds.
getDrugActivityRepeatData
                        Returns a matrix containing repeat activity
                        experiment data for a compound.
getDrugMoaList          Get a list of applicable MOA strings for a
                        drug.
getDrugName             Get the drug names for a set of NSC
                        identifiers.
getESetList             Returns a list of eSet objects.
getESetList,MolData-method
                        Returns a list of eSet objects.
getFeatureAnnot         Returns a list of data frames with feature
                        information.
getFeatureAnnot,DrugData-method
                        Returns a list of data frames with feature
                        information.
getFeatureAnnot,MolData-method
                        Returns a list of data frames with feature
                        information.
getFeatureDataFromMatList
                        Extract from a list of matrices the data
                        associated with a set of features.
getFingerprintList      Get a list of fingerprints for a set of
                        compounds
getMedSenLineActivity   Returns a vector of median sensitive cell line
                        activity (-logGI50) values for a set of
                        compounds.
getMinDrugActivityRepeatCor
                        Returns a table indicating, for each compound
                        in a specified set, the least significant
                        correlation and associated p-value between its
                        replicate experiments.
getMoaStr               Get MOA string
getMoaToCompounds       Get a named list mapping MOA classes to
                        associated compound sets.
getMolDataMatrices      Returns a list of molecular data type matrices,
                        with rownames in each matrix prefixed with a
                        data type abbreviation.
getMolDataType          Get the molecular data type prefixes for a set
                        of features.
getNumDrugActivityRepeats
                        Returns a vector indicating the number of drug
                        activity repeat experiments with available data
                        for each member of a set of compounds.
getNumMissingLines      Returns a vector indicating the number of
                        NCI-60 cell lines with missing activity data
                        for set of compounds.
getRepeatAct            Returns an eSet object with drug repeat
                        activity experiment data.
getRepeatAct,DrugData-method
                        Returns an eSet object with drug repeat
                        activity experiment data.
getRsd                  Computes the relative standard deviation values
                        with respect to the columns of a matrix or
                        data.frame.
getSampleData           Returns a data frame with sample information.
getSampleData,DrugData-method
                        Returns a data frame with sample information.
getSampleData,MolData-method
                        Returns a data frame with sample information.
getSmiles               Get the SMILES strings for a set of NSC
                        identifiers.
hasMoa                  Check if NSC has Mechanism of Action (MOA)
                        Annotation
initialize,DrugData-method
                        Returns a DrugData object.
initialize,MolData-method
                        Returns a MolData object.
isPublic                Check if an NSC ID is public
loadCellminerPlotInfo   Returns data to plot CellMiner plots
loadNciColorSet         Returns a 60-element color set that matches the
                        color set used on http://discover.nci.nih.gov/
parCorPatternComparison
                        Compare an input pattern against a set of
                        patterns, excluding the predictive effect of a
                        fixed pattern or set of patterns.
passRuleOf5             Checks if SMILES passes Lipinski's Rule of 5
passRuleOf5FromNsc      Checks if NSC passes Lipinski's Rule of 5
patternComparison       Compare an input pattern against a set of
                        patterns.
plotCellMiner           Description: Produces CellMiner-like plots in R
plotCellMiner2D         Make a simple 2d plot using two variables with
                        ggplot2
plotDrugActivityRepeats
                        Plot NCI-60 drug activity profiles for repeat
                        experiments.
plotDrugSets            Produces a barplot of the average values for a
                        set of NSCs with a error bar (one standard
                        deviation)
plotStructures          Plot Structures
plotStructuresFromNscs
                        Plot the structures for NSCs
rcdkplot                Plot molecules
removeMolDataType       Remove molecular data type prefixes from
                        features.
restrictFeatureMat      Restricts a feature matrix to only include
                        features associated with a specified gene set.
rowCors                 Row-wise correlations
runShinyApp             Run Shiny App
runShinyComparePlots    Run the Compare Plots Shiny App
runShinyCompareStructures
                        Run the Compare Structures Shiny App
runShinyCompoundBrowser
                        Run the Compound Browser
searchForNscs           Search for NSCs
selectCorrelatedRows    Select features that are correlated with a
                        given feature (or one or more features from a
                        set of features).
selectCorrelatedRowsFromMatrices
                        Select features that are correlated with a
                        given feature (or one or more features from a
                        set of features), merging results from multiple
                        candidate feature matrices.
