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 |
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