Introduction to cgdsclj

Clojure based API for accessing the Cancer Genomics Data Server (CGDS).

Table of Contents

• Introduction
• Installation
• Usage

Introduction

cgdsclj based API for accessing the Cancer Genomics Data Server (CGDS). It's based on cgdsr. Queries the CGDS API and returns available cancer studies. Input is a CGDS object and output is an array with information regarding the different cancer studies.

Installation

cgdsclj is available as a Maven artifact from Clojars.

With Leiningen/Boot:

[cgdsclj "0.1.0"]

cgdsclj supports clojure 1.8.0 and higher.

Usage

To use cgdsclj:

(require '[cgdsclj "0.1.0" as cgds])

(def base-url "http://www.cbioportal.org/")

# get cancer study
(def cancer-studies (cgds/cancer-studies base-url))
(cgds/list->map cancer-studies)

# get case list
(case-lists base-url "um_qimr_2016")

# get genetic profile
(genetic-profiles base-url "um_qimr_2016")

Contact

Jingcheng Yang yjcyxky@163.com

Your feedbacks are welcome. If you're struggling using the librairy, the best way to ask questions is to use the Github issues so that they are shared with everybody.

License

Copyright © 2019 Choppy Team. https://github.com/orgs/go-choppy/teams/choppy-team

This program and the accompanying materials are made available under the terms of the Eclipse Public License 2.0 which is available at http://www.eclipse.org/legal/epl-2.0.

This Source Code may also be made available under the following Secondary Licenses when the conditions for such availability set forth in the Eclipse Public License, v. 2.0 are satisfied: GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version, with the GNU Classpath Exception which is available at https://www.gnu.org/software/classpath/license.html.