$.shaidyRepo            Provide a simpler method for accessing repo
                        methods
+                       Add an Axis to an NG-CHM Version 2
NGCHM                   Next Generation Clustered Heat Map (NGCHM)
                        Construction Library
NGCHM-functions         Javascript extensions for the Next Generation
                        Clustered Heat Map (NGCHM) Construction Library
NGCHM-initialization    Initialization of the NGCHM library.
castAsInteger           Helper function to cast variables as integers.
castListAsInteger       Helper function to cast list as integer
chmAdd                  Add a list of objects to a NGCHM.
chmAddAxisType          Add an axis type to a NGCHM.
chmAddCSS               Add custom CSS to a NGCHM.
chmAddColormap          Add a colormap to a NGCHM.
chmAddCovariate         Add a covariate to an auxiliary dataset.
chmAddCovariateBar      Add a covariate bar to a NGCHM.
chmAddDataset           Add an auxiliary dataset to a NGCHM.
chmAddDialog            Add an extra dialog to a NGCHM.
chmAddLayer             Add a Layer to a NGCHM.
chmAddMenuItem          Add a menu entry to a NGCHM.
chmAddMetaData          Add MetaData to NG-CHM
chmAddOverview          Generate an overview image of the NGCHM when
                        making it.
chmAddPCA               Add PCA coordinates to an NG-CHM.
chmAddProperty          Add custom property to a NGCHM.
chmAddReducedDim        Add reduced dimension coordinates to an NG-CHM.
chmAddRelated           Add a link to related information to the NGCHM.
chmAddRelatedGroup      Add a group of related links to the NGCHM.
chmAddSpecificAxisTypeFunction
                        Add a CHM-specific axis type function to a
                        NGCHM.
chmAddTSNE              Add TSNE coordinates to an NG-CHM.
chmAddTag               Add tags to a NGCHM.
chmAddTemplate          Add a file template to the NGCHM.
chmAddToolboxR          Add standard toolbox to an NG-CHM axis
chmAddToolboxR2         Add Toolbox R2 to NG-CHM
chmAddToolboxRC         Add Toolbox RC to NG-CHM
chmAddUMAP              Add UMAP coordinates to an NG-CHM.
chmAddUWOT              Add UWOT::UMAP coordinates to an NG-CHM.
chmAxis                 Create a new Axis for adding to an NG-CHM.
chmAxisType             Create a new AxisType for adding to an
                        ngchmAxis.
chmBindFunction         Bind values to an existing JS function.
chmBrowse               Browse the NGCHMs on the specified server in
                        the viewer.
chmColOrder<-           Set the column order of data shown in a NGCHM.
chmColorMap             Get the color map of an NG-CHM object.
chmColorMap<-           Set the color map of an NG-CHM object
chmColors               Get the colors of an ngchmColormap, ngchmLayer,
                        ngchmBar, or ngchmCovariate.
chmColors<-             Set the colors of an ngchmColormap, ngchmLayer,
                        ngchmBar, or ngchmCovariate.
chmCovariate            Get a covariate attached to an NG-CHM dataset.
chmCovariateBar         Get a covariate bar attached to an NG-CHM.
chmCreateCollection     Create a new NG-CHM Collection
chmCreateManagedServer
                        Create an ngchmServer object for a managed
                        NG-CHM server
chmCreateServer         Create an ngchmServer object from a
                        specification.
chmCurrentCollection    Get the user's current collection
chmCurrentServer        Get the user's current server
chmDefaultColOrder      Return default column order of an NGCHM
chmDefaultRowOrder      Return default row order of an NGCHM
chmDeployServer         Get the name of a NGCHM server.
chmExportToFile         Export a standalone NGCHM to a file.
chmExportToHTML         Export a standalone HTML containing the NGCHM
                        to a file.
chmExportToPDF          Export a PDF of the NGCHM to a file.
chmFieldAccessFunction
                        Get Javascript function name for accessing a
                        specific string field in each element of string
                        vector.
chmGetDataset           Get the dataset from an NG-CHM object
chmGetDeployServerConfig
                        Get per-user configuration for a specific
                        deploy Server.
chmGetFunction          Get a predefined Javascript function for use in
                        NGCHM menus
chmGetOverview          Get the file path to the specified overview
                        file.
chmGetProperty          Get Property from NG-CHM
chmGetTypeInfo          Get information about a type name.
chmGetURL               Get the URL for an installed NGCHM.
chmHasProperty          Determine if the NG-CHM has the given property.
chmInstall              Add an NG-CHM to an NG-CHM collection.
chmLabel                Get the label/name of an NG-CHM object.
chmLabel<-              Set the label/name of an NG-CHM object
chmLayer                Get a specified Data Layer from an NG-CHM.
chmLayer<-              Set (or append) a specified Data Layer in an
                        NG-CHM.
chmListFunctions        List the predefined Javascript functions
                        available for use in NGCHM menus.
chmListServers          List NG-CHM Servers
chmListTypes            List known axis types.
chmLoadCHM              Load CHM from NG-CHM server
chmLoadShaidyCHM        Load an NG-CHM from an NG-CHM server.
chmMake                 Compile a NGCHM.
chmMakePrivate          Make NG-CHM Private on Server
chmMakePublic           Make NG-CHM Public on Server
chmManager              Open the NG-CHM Manager
chmName                 Get the name of a NGCHM.
chmNew                  Create a new NGCHM.
chmNewColorMap          Create a new Color Map for use in constructing
                        a NGCHM
chmNewCovariate         Create a new Covariate for adding to an NGCHM
                        auxilary dataset.
chmNewCovariateBar      Create a new covariate Bar for a NGCHM
chmNewDataLayer         Create a new Data Layer for a NGCHM.
chmNewDataset           Create a new Dataset for a NGCHM.
chmNewDialog            Create a new Dialog for a NGCHM.
chmNewFunction          Create a new Javascript function for adding to
                        a NGCHM menu.
chmNewProperty          Create a new Property for adding to a NGCHM.
chmNewServer            Create a new object representing a NGCHM
                        server.
chmOriginalColOrder     Return original column order of an NGCHM
chmOriginalRowOrder     Return original row order of an NGCHM
chmProperties           Create NG-CHM Properties
chmProperty             Get the value of an NG-CHM property.
chmProperty<-           Set the value of an NG-CHM property.
chmRandomColOrder       Return random column order of an NGCHM
chmRandomRowOrder       Return random row order of an NGCHM
chmRegisterAxisFunction
                        Register a predefined Javascript function for
                        use in NGCHM Axis menus.
chmRegisterFunction     Register a predefined Javascript function for
                        use in NGCHM menus.
chmRegisterGetMetadataFunction
                        Define and register a Javascript function for
                        obtaining a specific metadata value.
chmRegisterMatrixFunction
                        Register a predefined Javascript function for
                        use in NGCHM Matrix menus.
chmRegisterToolboxFunction
                        Register a Javascript function for use in the
                        NGCHM toolbox.
chmRegisterType         Register a type name.
chmRegisterTypeMapper   Register a predefined Javascript function for
                        converting values from one type to another.
chmRegisterTypeSplitter
                        Define and register a Javascript function for
                        converting a lists of type values into single
                        values.
chmRowOrder<-           Set the row order of data shown in a NGCHM.
chmServer               Get a registered ngchmServer object for use in
                        making and installing NGCHMs
chmSetCollection        Set the user's current server and/or collection
chmSetCredentials       Set Access Credentials for NG-CHM Server
chmSetDeployServerConfig
                        Specify per-user configuration for a specific
                        deploy Server.
chmStringopFunction     Get Javascript function name for performing a
                        specific string operation on each element of a
                        string vector.
chmTreeGaps             Creates new treeCuts object
chmUninstall            Remove an NG-CHM from Server
chmUrlBase              Get the base URL for a NGCHM installed on a
                        NGCHM server.
chmWriteCustomJS        Output Javascript code required to customize an
                        NGCHM.
getDimensions           Generic method to get a dimensions matrix from
                        obj.
gitHashObject           Obtain the git hash of an existing file.
initLogging             Initialize Logging
ngchm-class             Class representing a Next Generation Clustered
                        Heat Map (NGCHM) under construction.
ngchmAddDatasetBlob     Add a data file to a local shaidy repository
ngchmAddMatrixToCollection
                        Add a matrix reference to a collection
ngchmAddObjectToCollection
                        Add an object reference to a collection
ngchmAxis-class         Class representing an axis of a Next Generation
                        Clustered Heat Map (NG-CHM).
ngchmAxisFunction-class
                        Class representing an axis function for Next
                        Generation Clustered Heat Map (NGCHM).
ngchmAxisType-class     Class representing a type attached to an axis
                        in a Next Generation Clustered Heat Map
                        (NGCHM).
ngchmBar-class          Class representing a Covariate Bar on a Next
                        Generation Clustered Heat Map (NGCHM).
ngchmCSS-class          Class representing custom CSS for a Next
                        Generation Clustered Heat Map (NGCHM).
ngchmCollectionInCollection
                        Recursively determine if collection uuid is
                        contained in collection A collecton always
                        contains itself.
ngchmCollectionTree     Create a recursive description of a collection
ngchmColormap-class     Class representing a Color Map on a Next
                        Generation Clustered Heat Map (NGCHM).
ngchmCovariate-class    Class representing a Covariate attached to a
                        Dataset
ngchmCreateServerProtocol
                        Create and register an NGCHM server protocol
                        implementation.
ngchmDataset-class      Class representing a Dataset attached to a
                        NGCHM
ngchmDialog-class       Class representing an addon dialog
ngchmFindRepo           Find a repository, if any, that contains the
                        requested shaid
ngchmGetDataFileShaid   Compute shaid for a data file
ngchmGetEnv             Get the ngchm environment (for debugging only).
ngchmGetHandleHTTR      Get a HTTR handle for the server's view/WS URL
ngchmGetLabels          Get the axis labels of a shaidy dataset or
                        dendrogram
ngchmGetLabelsStr       Get the axis labels of a shaidy dataset or
                        dendrogram
ngchmGetProtoParam      Get Protocol Parameter for NG-CHM Server
ngchmGetServerProtocol
                        Get Server Protocol for NG-CHM
ngchmInitShaidyRepository
                        Initialize Shaidy Repository for NG-CHM
ngchmJS-class           Class representing a custom Javascript function
                        for a Next Generation Clustered Heat Map
                        (NGCHM).
ngchmLayer-class        Class representing a Layer on a Next Generation
                        Clustered Heat Map (NGCHM).
ngchmListServerProtocols
                        List defined server protocols
ngchmLoadDatasetBlob    Load a data matrix from a local shaidy
                        repository
ngchmMakeFormat.original
                        Make an original format NGCHM.
ngchmMakeFormat.shaidy
                        Make a shaidy format NGCHM.
ngchmMatrixFunction-class
                        Class representing a matrix function for Next
                        Generation Clustered Heat Map (NGCHM).
ngchmMenuItem-class     Class representing a Menu Item for a Next
                        Generation Clustered Heat Map (NGCHM).
ngchmMetaData-class     Class representing meta data attached to an
                        NG-CHM
ngchmNewBar             Create a new Classification Bar for a NGCHM
ngchmNewCollection      Create a new collection in a local shaidy
                        repository
ngchmOverview-class     Class representing an overview of a Next
                        Generation Clustered Heat Map (NGCHM).
ngchmProperty-class     Class representing a Generic Property for a
                        Next Generation Clustered Heat Map (NGCHM).
ngchmProtoParamCheck    Check Protocol Parameters for NG-CHM
ngchmPushSourceRepository
                        Push a local shaidy repository onto the stack
                        of source repositories
ngchmPushSourceServer   Push a shaidy server onto the stack of source
                        repositories
ngchmPushTempRepository
                        Push Temporary Repository for NG-CHM
ngchmRegisterServer     Register an ngchmServer.
ngchmRelated-class      Class representing a link related to a NGCHM
ngchmRelatedGroup-class
                        Class representing a group of related links to
                        a NGCHM
ngchmRenderChm          Render a shaidy NGCHM
ngchmResponseJSON       Return response content interpreted as JSON
ngchmRowCenter          Row center a shaidy dataset
ngchmSaveAsDatasetBlob
                        Save a numeric matrix as a blob in a shaidy
                        repository
ngchmSaveAsDendrogramBlob
                        Save a dendrogram as a blob in a shaidy
                        repository
ngchmSaveChmAsBlob      Save an NGCHM as a shaidy blob
ngchmServer-class       Class representing a Next Generation Clustered
                        Heat Map (NGCHM) server.
ngchmServerProtocol-class
                        Class representing a deployment method for a
                        Next Generation Clustered Heat Map (NGCHM)
                        server.
ngchmTemplate-class     Class representing a Template attached to a
                        NGCHM
ngchmTileDataset        Get the tiles for a shaidy dataset
ngchmTypeMapper-class   Class representing a type mapper function for
                        Next Generation Clustered Heat Map (NGCHM).
ngchmUnregisterServer   Unregister NG-CHM Server
ngchmValueProp-class    Class representing the properties of a data
                        point in a Next Generation Clustered Heat Map
                        (NGCHM).
ngchmVersion2-class     Class representing ngchmVersion2 object
optDendrogram-class     Optional Dendrogram
plot.ngchmVersion2      Open the NG-CHM on the specified server in the
                        viewer.
print.ngchm.type.info   Pretty Print NGCHM Type Information
print.shaidyRepo        Print a shaidy repository
shaid-class             Class representing the shaid of an object
shaidyAddFileBlob       Add data file(s) and properties to a local
                        shaidy repository
shaidyBlobExists        Determine if one more blobs exist in a shaidy
                        repository
shaidyCopyBlob          Copy a blob from one repository to another
shaidyCreateProtoBlob   Create a prototype blob in a shaidy repository
shaidyFinalizeProtoBlob
                        Finalize a prototype blob
shaidyFindRepo          Find the first repository, if any, that
                        contains the requested shaid
shaidyGetComponents     Get an object's component shaids
shaidyGetShaid          Get shaid for an object
shaidyHashProtoBlob     Compute the shaid to assign a protoblob
shaidyInitRepository    Create and initialize Shaidy Repository
shaidyLoadProvenanceDB
                        Load the provid -> shaid DB for a local shaidy
                        repository
shaidyLoadProvidDB      Load the provid -> labels DB for a local shaidy
                        repository.
shaidyLoadRepository    Load a shaidy repository
shaidyNewCache          Create in memory shaid cache
shaidyProvenance        Create a provid from a list of label values
shaidyRepoAPI           Get the methods for the repository API called
                        api
treeCuts-class          Helper class for setting row/col gap locations
                        as tree cuts
verifyNumeric           Helper function to verify if variable is
                        numeric.
