cgds

CGDS-JS

A Node.js and browser module for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC). Read more about this service at the cBio Cancer Genomics Portal.

Example

var CGDS, cgds;
CGDS = require("cgds");
cgds = new CGDS();
cgds.getMutationData("brca_tcga_mutations", ["TP53", "GATA3"], "brca_tcga_all", function (err, res) {
    console.log(res);
});

Usage

Node.js

• Install it:

   npm install cgds
  

• Require it:

   var CGDS = require("cgds");
  

• Instantiate a CGDS client:

   var cgds = new CGDS();
  

• See below for a list of methods.

Browser

• Include it:

   <script src="http://agrueneberg.github.io/CGDS-JS/cgds.min.js"></script>
  

• Require it:

   var CGDS = require("cgds");
  

• Instantiate a CGDS client (you will need a CORS proxy such as Proxer for this):

   var cgds = new CGDS({
       proxy: "http://example.com/corsproxy?url="
   });
  

• See below for a list of methods.

Methods

See Web API for more details.

getTypesOfCancer

Retrieves a list of all the clinical types of cancer.

Parameters

• callback

getCancerStudies

Retrieves meta-data regarding cancer studies.

Parameters

• callback

getGeneticProfiles

Retrieves meta-data regarding all genetic profiles, e.g. mutation or copy number profiles, stored about a specific cancer study.

Parameters

• cancer_study_id
• callback

getCaseLists

Retrieves meta-data regarding all case lists stored about a specific cancer study.

Parameters

• cancer_study_id
• callback

getProfileData

Retrieves genomic profile data for one or more genes.

Parameters

• case_set_id
• genetic_profile_id
• gene_list
• callback

getMutationData

Retrieves the full set of annotated extended mutation data.

Parameters

• genetic_profile_id
• gene_list
• case_set_id (optional)
• callback

getClinicalData

Retrieves overall survival, disease free survival and age at diagnosis for specified cases.

Parameters

• case_set_id
• callback