Introduction to cgdsclj

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

NOTE: It's an unstable version, NOT RECOMMENDED for production use.

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])

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

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

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

# get clinical data
(clinical-data ["um_qimr_2016_all"] :case-set-id)

# get profile data
(profile-data ["EGFR"] "um_qimr_2016_mutations" ["um_qimr_2016_all"] :case-set-id)

Advanced Usage

# You may want to change headers and base-url for each http request.

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

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

(def headers
  {:content-type :json
   :connection-timeout 10000
   :accept :json})

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

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

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

# get clinical data
(clinical-data ["um_qimr_2016_all"] :case-set-id base-url headers)

# get mutation data
(mutation-data "um_qimr_2016" "um_qimr_2016_all" "um_qimr_2016_mutations" ["EGFR"])

# get profile data
(profile-data ["EGFR"] ["um_qimr_2016_mutations"] ["um_qimr_2016_all"] :case-set-id base-url headers)

Contact

Jingcheng Yang [email protected]

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.