node package manager

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

  1. Install it:

     npm install cgds
    
  2. Require it:

     var CGDS = require("cgds");
    
  3. Instantiate a CGDS client:

     var cgds = new CGDS();
    
  4. See below for a list of methods.

Browser

  1. Include it:

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

     var CGDS = require("cgds");
    
  3. 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="
     });
    
  4. 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
  1. callback

getCancerStudies

Retrieves meta-data regarding cancer studies.

Parameters
  1. callback

getGeneticProfiles

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

Parameters
  1. cancer_study_id
  2. callback

getCaseLists

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

Parameters
  1. cancer_study_id
  2. callback

getProfileData

Retrieves genomic profile data for one or more genes.

Parameters
  1. case_set_id
  2. genetic_profile_id
  3. gene_list
  4. callback

getMutationData

Retrieves the full set of annotated extended mutation data.

Parameters
  1. genetic_profile_id
  2. gene_list
  3. case_set_id (optional)
  4. callback

getClinicalData

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

Parameters
  1. case_set_id
  2. callback