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