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.
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);
});
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Install it:
npm install cgds
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Require it:
var CGDS = require("cgds");
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Instantiate a CGDS client:
var cgds = new CGDS();
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See below for a list of methods.
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Include it:
<script src="http://agrueneberg.github.io/CGDS-JS/cgds.min.js"></script>
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Require it:
var CGDS = require("cgds");
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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=" });
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See below for a list of methods.
See Web API for more details.
Retrieves a list of all the clinical types of cancer.
callback
Retrieves meta-data regarding cancer studies.
callback
Retrieves meta-data regarding all genetic profiles, e.g. mutation or copy number profiles, stored about a specific cancer study.
cancer_study_id
callback
Retrieves meta-data regarding all case lists stored about a specific cancer study.
cancer_study_id
callback
Retrieves genomic profile data for one or more genes.
case_set_id
genetic_profile_id
gene_list
callback
Retrieves the full set of annotated extended mutation data.
genetic_profile_id
gene_list
case_set_id
(optional)callback
Retrieves overall survival, disease free survival and age at diagnosis for specified cases.
case_set_id
callback