Department of Bioinformatics and Computational Biology

ESTIMATE:Overview

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ESTIMATE

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ESTIMATE
Overview
Description A tool for predicting tumor purity, and the presence of infiltrating stromal/immune cells in tumor tissues using gene expression data.
URL http://bioinformatics.mdanderson.org/estimate/
Development Information
Language R (package), DHTML (website)
Current Version 1.0.13
License GPL-2 (package)
Status Active
Last Updated 2016-09-26
References
Citations Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W, Treviño V, Shen H, Laird PW, Levine DA, Carter SL, Getz G, Stemke-Hale K, Mills GB, Verhaak R. (2013).
"Inferring tumour purity and stromal and immune cell admixture from expression data."
Nature Communications 4, 2612
doi:10.1038/ncomms3612.
News As of July/August 2016, this highly cited paper received enough citations to place it in the top 1% of the academic field of Clinical Medicine for the field and publication year.
Help and Support
Contact P. Roebuck[1]


ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) is a tool for predicting tumor purity, and the presence of infiltrating stromal/immune cells in tumor tissues using gene expression data. ESTIMATE algorithm is based on single sample Gene Set Enrichment Analysis and generates three scores:

1) stromal score (that captures the presence of stroma in tumor tissue),
2) immune score (that represents the infiltration of immune cells in tumor tissue), and
3) estimate score (that infers tumor purity).

The website presents the scores for all TCGA tumor types.

Contents


Browser Requirements

ESTIMATE website is compatible with latest versions of all major browsers, including Chrome, Safari, and Firefox. Javascript must be enabled by the browser.

Usage

Login is not required — it is free for anyone to use.

Web Site Release History

  • Version 2.0.0 was released on 2016-01-22 with 25 disease types.
  • Version 1.0.0 was released on 2013-05-23 with 10 disease types.

R Package

In early October 2016, the ESTIMATE R package was migrated to R-Forge, available here.

Installation

R script:

library(utils)
rforge <- "http://r-forge.r-project.org"
install.packages("estimate", repos=rforge, dependencies=TRUE)


Support

For questions or support related to the use of either the ESTIMATE R package *or* website, please visit on the project's forum page.
For other inquiries, please contact Kosuke Yoshihara.

Disclaimer

This website is for educational and research purposes only.