TCGA Toolbox

TCGA Toolbox provides a scripting environment to retrieve, store, and analyze data from The Cancer Genome Atlas (TCGA) in the browser. It can be extended by loading modules, or used interactively from the browser's JavaScript console.

This is a work in progress. The code is hosted on GitHub.

TCGA Toolbox can be extended by loading remote scripts—either by specifying the URL or by selecting one from our trusted authors.

Load module by URL

Load module by author

Loaded modules

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TCGA Toolbox provides some useful functions scoped in the global TCGA namespace to interact with TCGA.

Unless stated otherwise, the first argument of a callback function is reserved for an error object, a useful convention to allow error catching in asynchronous programming. If an error object is null no error occurred.

Load scripts

`TCGA.loadScript(url, callback)`	Loads one or more scripts over HTTPS (HTTP is not supported) using HTML script elements. `url` is a string or a string array of URLs, `callback` a function with two parameters, an error object and a string array of loaded scripts.
`TCGA.modules(callback)`	Returns a list of loaded modules. `callback` is a function with two parameters, an error object and a string array of loaded modules.

Find data

`TCGA.find(query, callback)`	Queries the TCGA RDF file index. `query` is a SPARQL query string, `callback` a function with two parameters, an error object and an object representing the SPARQL query results in the SPARQL 1.1 Query Results JSON Format.

Get data

`TCGA.get(url, callback)`	Downloads the contents of a file from TCGA's open-access HTTP directory or any other data provider. `url` is a URL string, `callback` a function with two parameters, an error object and a string representing the contents of the requested file.
`TCGA.get.json(url, callback)`	Same as `TCGA.get`, but parses the downloaded file to JSON. `url` is a URL string, `callback` a function with two parameters, an error object and an object representing the contents of the requested file as JSON.
`TCGA.get.xml(url, callback)`	Same as `TCGA.get`, but parses the downloaded file to XML. `url` is a URL string, `callback` a function with two parameters, an error object and an object representing the contents of the requested file as XML.
`TCGA.get.sparql(url, callback)`	Same as `TCGA.get`, but parses the downloaded file to the SPARQL 1.1 Query Results JSON Format. `url` is a URL string, `callback` a function with two parameters, an error object and an object representing the SPARQL query results as JSON.
`TCGA.get.range(url, startByte, endByte, callback)`	Same as `TCGA.get`, but downloads only a subset of the file within the specified byte range. `url` is a URL string, `startByte` and `endByte` the integer range of bytes to download, and `callback` a function with two parameters, an error object and a string representing the partial contents of the requested file.
`TCGA.get.archive(url, callback)`	Same as `TCGA.get`, but extracts the downloaded gzipped archive. `url` is a URL string, `callback` a function with two parameters, an error object and an object representing the contents of the requested archive.
`TCGA.get.barcodes(uuids, callback)`	Maps UUIDs to barcodes using the TCGA Barcode to UUID Web Service. `uuids` is an array of UUIDs, `callback` a function with two parameters, an error object and an object representing the mapping.
`TCGA.get.uuids(barcodes, callback)`	Maps barcodes to UUIDs using the TCGA Barcode to UUID Web Service. `barcodes` is an array of barcodes, `callback` a function with two parameters, an error object and an object representing the mapping.

Store data

Info We recommend to prefix all keys with the name of your module, e.g. module:key.

`TCGA.data.set(key, value, callback)`	Adds a key-value pair to the store. `key` is a string representing the key, `value` any type representing the value, and `callback` a function with one parameter, an error object.
`TCGA.data.get(key, callback)`	Retrieves a key-value pair from the store. `key` is a string representing the key, `callback` a function with two parameters, an error object and any type representing the value.
`TCGA.data.del(key, callback)`	Removes a key-value pair from the data. `key` is a string representing the key, `callback` a function with one parameter, an error object.
`TCGA.data.exists(key, callback)`	Checks if a key-value pair with the specified key exists in the store. `key` is a string representing the key, `callback` a function with two parameters, an error object and a boolean indicating if it is in the store or not.
`TCGA.data.keys(callback)`	Returns a list of all keys in the stores. `callback` is a function with two parameters, an error object and a string array of keys.
`TCGA.data.clear(callback)`	Removes all key-value pairs from the store. `callback` is a function with one parameter, an error object.

User Interface

Load external stylesheets

`TCGA.ui.loadStylesheet(url)`	Loads one or more external stylesheets using HTML link elements. `url` is a string or a string array of URLs.

Register tab in main menu

`TCGA.ui.registerTab(options, callback)`	Registers a tab in the menu bar of the TCGA Toolbox. `options` is an object with the following properties: `id` is a string representing the ID of the tab (we recommend to name it after your module), `title` is a string representing the title of your module, `content` is the HTML fragment describing the tab pane, and `switchTab` is a boolean indicating whether the TCGA Toolbox should immediately switch to your tab after it was created. `callback` is a function with two parameters, an error object and the DOM element of the created tab pane.

Display notifications

`TCGA.ui.toast.info(message, duration)`	Displays an info notification with the specified string `message` for the specified `duration` in milliseconds.
`TCGA.ui.toast.success(message, duration)`	Displays a success notification with the specified string `message` for the specified `duration` in milliseconds.
`TCGA.ui.toast.error(message, duration)`	Displays an error notification with the specified string `message` for the specified `duration` in milliseconds.