R/MATLAB Packages

CGDS-R Package

Description

The CGDS-R package provides a basic set of functions for querying the Cancer Genomic Data Server (CGDS) via the R platform for statistical computing.

Maintained by Anders Jacobsen at the Computational Biology Center, MSKCC.

Documentation

Installation

  1. The CDGS-R package currently only works with R Version 2.12 or higher.

  2. Then install the cgds-R package from within R:

    install.packages('cgdsr')

Example usage

# Create CGDS object
mycgds = CGDS("http://www.cbioportal.org/public-portal/")

test(mycgds)

# Get list of cancer studies at server
getCancerStudies(mycgds)

# Get available case lists (collection of samples) for a given cancer study
mycancerstudy = getCancerStudies(mycgds)[2,1]
mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]

# Get available genetic profiles
mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[4,1]

# Get data slices for a specified list of genes, genetic profile and case list
getProfileData(mycgds,c('BRCA1','BRCA2'),mygeneticprofile,mycaselist)

# Get clinical data for the case list
myclinicaldata = getClinicalData(mycgds,mycaselist)

# documentation
help('cgdsr')
help('CGDS')

MATLAB CGDS Cancer Genomics Toolbox

Description

This toolbox provides direct access to cancer genomics data from within the MATLAB environment. The toolbox will query the Cancer Genomics Data Server Web API, and return data in a structured format.

Maintained by Erik Larsson at the Computational Biology Center, MSKCC.

A tutorial ('showdemo cgdstutorial') makes it easy to get started.

Download

CGDS Toolbox @ MATLAB Central

Documentation

Complete CGDS Tutorial

Example Usage

Like the R package, the CGDS MATLAB toolbox provides a set of functions for direct retrieval of portal data from within the MATLAB (MathWorks Inc.) environment. Each toolbox function has a direct counterpart in the CGDS Web API. Data is returned as structured arrays, in a format that is easy to interpret and ready for subsequent visualization and statistical analysis.

An included tutorial ("showdemo cgdstutorial") shows how to use all the functions, as well as how to make basic plots.

% Get started by adding the CGDS toolbox directory to the path (this will depend
% on install location) and setting the server URL
addpath('/MATLAB/cgds');
cgdsURL = 'http://www.cbioportal.org/public-portal';

% Show toolbox help ('helpwin cgds' will open in the Help window)
help cgds;

% Get list of cancer studies at server
cancerStudies = getcancerstudies(cgdsURL);

% Get available genetic profiles for a given cancer type (GBM below)
geneticProfiles = getgeneticprofiles(cgdsURL, cancerStudies.cancerStudyId{2});

% Get available case lists (collections of samples)
caseLists = getcaselists(cgdsURL, cancerStudies.cancerStudyId{2});

% Get multiple types of genetic profile data for p53 in GBM
profileData = getprofiledata(cgdsURL, caseLists.caseListId{2}, ...
                            geneticProfiles.geneticProfileId([3 4]), ...
                            'TP53', true);

% Plot mRNA levels as a function of copy number status
boxplot(profileData.data(2,:),profileData.data(1,:));
title('TP53'); xlabel('Copy-number status'); ylabel('mRNA level');

% Get clinical data for all patients in a given case list
clinicalData = getclinicaldata(cgdsURL, caseLists.caseListId{2});

% Run a function in non-verbose mode
cancerStudies = getcancerstudies(cgdsURL, 'silent');

What's New

We are hiring a Front End Engineer
We are hiring a Data Curator
New data and features released

    Sign up for low-volume email news alerts:
    
    Or follow us @cbioportal on Twitter

Data Sets

The Portal contains data for 17181 tumor samples from 69 cancer studies. [Details.]

Example Queries

RAS/RAF alterations in colorectal cancer

BRCA1 and BRCA2 mutations in ovarian cancer

POLE hotspot mutations in endometrial cancer

Protein changes in PTEN-altered ovarian cancer samples

TP53 and MDM2/4 alterations in GBM

PTEN mutations in GBM in text format

BRAF V600E mutations across cancer types

Patient view of an endometrial cancer case

What People are Saying

  "Whenever bench scientists ask me how they can look at TCGA data, I've never had a good answer for them. Now I do. The cBio Portal meets a critical need--it is the interface that the cancer research community needs to access the wealth of TCGA. Even as a computational biologist, I use it to follow-up on genes of interest. It makes querying the data much less painful."

– Postdoctoral Fellow, Oregon Health & Science University

  "I would like to congratulate you and the team of the cBio portal. It's just an amazing tool to work with, and we at Mass General really appreciate it."

– Research Fellow at Massachusetts General Hospital

  "As a bench biologist with primary aim of determining gene aberrations in GBM, I found your site absolutely fantastic! Thank you! I have to reiterate how awesome and user-friendly your group has made this site - finally accomplishing the goal of having data easily accessible and meaningful."

– Sr. Research Associate at Knight Cancer Institute/OHSU

  "Thank you for your incredible resource that has helped greatly in accessing the TCGA genomics data."

– Postdoctoral Fellow, Johns Hopkins University School of Medicine, Dept Radiation Oncology and Molecular Radiation Sciences

  "I have been enjoying the ease with which TCGA data can be extracted in R using your CGDS package. Very nice work!"

– Sr. Software Engineer, Institute for Systems Biology

  "Thank you for generating such an excellent software. It is very useful for our research."

– Research Fellow, Memorial Sloan-Kettering Cancer Center

  "Thank you very much for providing and maintaining this great resource."

– Scientist, Discovery Bioinformatics, Biotechnology Company

  "I want to thank you for the nice, useful and user-friendly interface you have generated and shared with the community."

– Postdoctoral Fellow, Harvard Medical School, Children's Hospital Boston

  "This portal is truly the greatest thing since sliced bread. I am making discoveries with it not only in glioblastoma, my primary focus, but in other cancers as well -- it's all so easy with this fantastic tool. And I am enjoying showing it to my colleagues, whose jaws also drop. Thank you a thousand times over for this beautiful public resource. I am looking forward to citing this soon in an upcoming paper..."

– Associate Professor, University of Virginia