| cash-.shaidyRepo | Provide a simpler method for accessing repo methods |
| castAsInteger | Helper function to cast variables as integers. |
| castListAsInteger | Helper function to cast list as integer |
| chmAddAxisType-method | Add an axis type to a NGCHM. |
| chmAddColormap-method | Add a colormap to a NGCHM. |
| chmAddCovariateBar-method | Add a covariate bar to a NGCHM. |
| chmAddCovariate-method | Add a covariate to an auxiliary dataset. |
| chmAddCSS-method | Add custom CSS to a NGCHM. |
| chmAddDataset-method | Add an auxiliary dataset to a NGCHM. |
| chmAddDialog-method | Add an extra dialog to a NGCHM. |
| chmAddLayer-method | Add a Layer to a NGCHM. |
| chmAddMenuItem-method | Add a menu entry to a NGCHM. |
| chmAddMetaData-method | Add meta data. |
| chmAdd-method | Add a list of objects to a NGCHM. |
| chmAddOverview-method | Generate an overview image of the NGCHM when making it. |
| chmAddPCA | Add PCA coordinates to an NG-CHM. |
| chmAddProperty-method | Add custom property to a NGCHM. |
| chmAddReducedDim | Add Single Cell reduced dimension coordinates to an NG-CHM. |
| chmAddRelatedGroup-method | Add a group of related links to the NGCHM. |
| chmAddRelated-method | Add a link to related information to the NGCHM. |
| chmAddSpecificAxisTypeFunction-method | Add a CHM-specific axis type function to a NGCHM. |
| chmAddTag-method | Add tags to a NGCHM. |
| chmAddTemplate-method | Add a file template to the NGCHM. |
| chmAddToolboxR2-method | Add standard toolbox to an element |
| chmAddToolboxRC-method | Add standard toolbox to an element |
| chmAddToolboxR-method | Add standard toolbox to an axis |
| chmAddTSNE | Add TSNE coordinates to an 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-method | Bind values to an existing JS function. |
| chmBrowse | Browse the NGCHMs on the specified server in the viewer. |
| chmColOrder-method | Set the column order of data shown in a NGCHM. |
| chmColorMap | Get the color map of an NG-CHM object. |
| chmColorMap-set | Set the color map of an NG-CHM object |
| chmColors | Get the colors of an ngchmColormap, ngchmLayer, ngchmBar, or... |
| chmColors-set | Set the colors of an ngchmColormap, ngchmLayer, ngchmBar, or... |
| chmCovariate | Get a covariate attached to an NG-CHM dataset. |
| chmCovariateBar | Get a covariate bar attached to an NG-CHM. |
| chmCreateCollection | Create a new 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-method | Get the name of a NGCHM server. |
| chmExportToFile-method | Export a standalone NGCHM to a file. |
| chmExportToHTML-method | Export a standalone HTML containing the NGCHM to a file. |
| chmExportToPDF-method | Export a PDF of the NGCHM to a file. |
| chmFieldAccessFunction | Get Javascript function name for accessing a specific string... |
| chmGetDataset-method | 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-method | Get a property value from an NG-CHM object |
| chmGetTypeInfo | Get information about a type name. |
| chmGetURL-method | Get the URL for an installed NGCHM. |
| chmHasProperty-method | Determine if the NG-CHM has the given property. |
| chmInstall-method | Add an NG-CHM to an NG-CHM collection. |
| chmLabel | Get the label/name of an NG-CHM object. |
| chmLabel-set | Set the label/name of an NG-CHM object |
| chmLayer | Get a specified Data Layer from an NG-CHM. |
| chmListFunctions | List the predefined Javascript functions available for use in... |
| chmListServers | Return the names of the NGCHM servers defined to date in this... |
| chmListTypes | List known axis types. |
| chmLoadCHM-method | Load CHM from NG-CHM server |
| chmLoadShaidyCHM | Load an NG-CHM from an NG-CHM server. |
| chmMake-method | Compile a NGCHM. |
| chmMakePrivate-method | Make an installed NGCHM private. |
| chmMakePublic-method | Make an installed NGCHM public. |
| chmManager | Manage the NGCHMs on the specified server in the viewer. |
| chmName-method | 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... |
| 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 a list of NGCHM properties. |
| chmProperty | Get the value of an NG-CHM property. |
| chmProperty-set | 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... |
| chmRegisterFunction | Register a predefined Javascript function for use in NGCHM... |
| chmRegisterGetMetadataFunction | Define and register a Javascript function for obtaining a... |
| chmRegisterMatrixFunction | Register a predefined Javascript function for use in NGCHM... |
| chmRegisterToolboxFunction | Register a Javascript function for use in the NGCHM toolbox. |
| chmRegisterType | Register a type name. |
| chmRegisterTypeMapper | Register a predefined Javascript function for converting... |
| chmRegisterTypeSplitter | Define and register a Javascript function for converting a... |
| chmRowOrder-method | Set the row order of data shown in a NGCHM. |
| chmServer | Get a registered ngchmServer object for use in making and... |
| chmSetCollection | Set the user's current server and/or collection |
| chmSetCredentials-method | Set access credentials. |
| chmSetDeployServerConfig | Specify per-user configuration for a specific deploy Server. |
| chmStringopFunction | Get Javascript function name for performing a specific string... |
| chmTreeGaps | Creates new treeCuts object |
| chmUninstall-method | Remove an installed NGCHM. |
| chmUrlBase-method | Get the base URL for a NGCHM installed on a NGCHM server. |
| chmUserDendrogramToShaid | Convert a user specified dendrogram to a shaid |
| chmUserLabelsToShaid | Convert user specified labels to a shaid |
| chmWriteCustomJS | Output Javascript code required to customize an NGCHM. |
| cos.dist1 | Compute cosine (angular) distance matrix |
| gitHashObject | Obtain the git hash of an existing file. |
| initLogging | Function to initialize logging |
| 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... |
| ngchmAxisFunction-class | Class representing an axis function for Next Generation... |
| ngchmAxisType-class | Class representing a type attached to an axis in a Next... |
| ngchmBar-class | Class representing a Covariate Bar on a Next Generation... |
| ngchm-class | Class representing a Next Generation Clustered Heat Map... |
| ngchmCollectionInCollection | Recursively determine if collection uuid is contained in... |
| ngchmCollectionTree | Create a recursive description of a collection |
| ngchmColormap-class | Class representing a Color Map on a Next Generation Clustered... |
| ngchmCovariate-class | Class representing a Covariate attached to a Dataset |
| ngchmCreateServerProtocol | Create and register an NGCHM server protocol implementation. |
| ngchmCSS-class | Class representing custom CSS for a Next Generation Clustered... |
| 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 |
| NGCHM-functions | Javascript extensions for the Next Generation Clustered Heat... |
| 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 a server protocol parameter |
| ngchmGetServerProtocol | Lookup a Server Protocol |
| NGCHM-initialization | Initialization of the NGCHM library. |
| ngchmInitShaidyRepository | Create a shaidy repository for NG-CHMS |
| ngchmJS-class | Class representing a custom Javascript function for a Next... |
| ngchmLayer-class | Class representing a Layer on a Next Generation Clustered... |
| 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... |
| ngchmMenuItem-class | Class representing a Menu Item for a Next Generation... |
| 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... |
| NGCHM-package | Next Generation Clustered Heat Map (NGCHM) Construction... |
| ngchmProperty-class | Class representing a Generic Property for a Next Generation... |
| ngchmProtoParamCheck | Check that all required parameters are specified, and all... |
| ngchmPushSourceRepository | Push a local shaidy repository onto the stack of source... |
| ngchmPushSourceServer | Push a shaidy server onto the stack of source repositories |
| ngchmPushTempRepository | Push a shaidy repository onto the stack of temporary... |
| 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... |
| ngchmServerProtocol-class | Class representing a deployment method for a Next Generation... |
| ngchmShaidyInit | Initialize shaidy subsystem for NGCHMs |
| 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... |
| ngchmUnregisterServer | Unregister ngchmServer(s). |
| ngchmValueProp-class | Class representing the properties of a data point in a Next... |
| 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 the result returned by chmGetTypeInfo. |
| print.shaidyRepo | Print a shaidy repository |
| readTile | Read a binary viewer tile as a matrix |
| 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... |
| shaidyGetComponents-method | Get an object's component shaids |
| shaidyGetShaid-method | Get shaid for an object |
| shaidyHashProtoBlob | Compute the shaid to assign a protoblob |
| shaidyInit | Initialize the shaidy subsystem |
| shaidyInitRepository | Create and initialize a local 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 |
| shaidyRegisterRepoAPI | Set the methods for the repository API called api |
| shaidyRepoAPI | Get the methods for the repository API called api |
| TCGA.GBM.EXPR | Sample dataset containing RNA expression data from Affymetrix... |
| treeCuts-class | Helper class for setting row/col gap locations as tree cuts |
| validateNewLayer | Check that the specified layer can be added to the specificed... |
| verifyNumeric | Helper function to verify if variable is numeric. |
| writeTile | Write a matrix as a binary viewer tile |
