Wolfram Language Paclet Repository

Community-contributed installable additions to the Wolfram Language

JaneShenGunther/TCGADataTool

(1.2.1) current version: 1.3.1 »

TCGA Data Tool retrieves TCGA cancer datasets easily from the NCI GDC and TCIA portals

Contributed by: Jane Shen-Gunther MD, PhD, Rutger S Gunther MD, and Wolfram Solutions

The TCGADataTool provides a user-friendly interface for retrieval of cancer datasets from The Cancer Genome Atlas (TCGA) data portals. The National Cancer Institute (NCI) Genomic Data Commons (GDC) data portal hosts a repository of clinical, biospecimen, genomics, and histological data from 67 primary tumor sites. The Cancer Imaging Archive (TCIA) portal hosts a large archive of radiological images from various clinical cancer projects to include TCGA. Retrieved data may be easily imported into Mathematica for analysis, visualization, machine learning, and other applications.

The current version uses the Cervical Cancer Dataset (TCGA-CESC) as a demonstration model.

Installation Instructions

To install this paclet in your Wolfram Language environment, evaluate this code:
PacletInstall["JaneShenGunther/TCGADataTool"]


To load the code after installation, evaluate this code:
Needs["JaneShenGunther`TCGADataTool`"]

Details

The TCGADataTool allows for exploration of cancer datasets from TCGA projects.
Version 13.0 or newer of the Wolfram Language is required.
Known issues: in windows, the UI can be displayed greatly magnified, requiring scrolling around the window to access many elements. This is due to an interaction between the magnification scaling options display of Mathematica documents. Please ensure that the windows scale option is set to 100% (Settings > System > Display, then scroll down to the dropdown menu under "Scale and Layout"). If the issue persists, further adjustments can be made using Mathematica's own magnification options, in the bottom right hand corner of any notebook.

Paclet Guide

Examples

Basic Examples

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Out[1]=

Publisher

Jane ShenGunther

Disclosures

  • Local files
  • External services
  • WL system configuration
  • WL built-in symbols
  • Local system interactions
  • Learn More »

Compatibility

Wolfram Language Version 13.0

Version History

  • 1.3.1 – 10 March 2023
  • 1.3.0 – 08 March 2023
  • 1.2.4 – 01 March 2023
  • 1.2.3 – 21 February 2023
  • 1.2.2 – 17 February 2023
  • 1.2.1 – 16 February 2023
  • 1.2.0 – 16 February 2023
  • 1.1.0 – 09 February 2023
  • 1.0.0 – 01 February 2023

License Information

MIT License

Paclet Source