cgds

CGDS-JS

A Node.js 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.

Usage

1. Install it:

    npm install cgds
   

2. Require it:

    var CGDS = require("cgds");
   

3. Instantiate a CGDS client:

    var cgds = new CGDS("http://www.cbioportal.org/public-portal/webservice.do");
   

4. See below for a list of methods.

Methods

See Web API for more details.

getTypesOfCancer(callback)

Retrieves a list of all the clinical types of cancer.

getCancerStudies(callback)

Retrieves meta-data regarding cancer studies.

getGeneticProfiles(cancer_study_id, callback)

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

getCaseLists(cancer_study_id, callback)

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

getProfileData(case_set_id, genetic_profile_id, gene_list, callback)

Retrieves genomic profile data for one or more genes.

getMutationData(genetic_profile_id, case_set_id, gene_list, callback)

Retrieves the full set of annotated extended mutation data.

getClinicalData(case_set_id, callback)

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