ESTIMATE
| Overview | |
|---|---|
| Description | A tool for predicting tumor purity, and the presence of infiltrating stromal/immune cells in tumor tissues using gene expression data. |
| Development Information | |
| URL | https://bioinformatics.mdanderson.org/estimate/ (opens in new tab) |
| Language | R (package), DHTML (website) |
| Current version | 1.0.13 |
| License | GPL-2 (package) |
| Status | Active |
| Last updated | 2016-09-26 |
| 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. |
| References | |
| Citation | 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 http://dx.doi.org/10.1038/ncomms3612 (opens in new tab) |
| Help and Support | |
| Contact | MDACC-Bioinfo-IT-Admin@mdanderson.org |
ESTIMATE
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 (opens in new tab) presents the scores for all TCGA tumor types.
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 (opens in new tab) 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 (opens in new tab).
Installation
R script:
library(utils)
rforge <- "http://r-forge.r-project.org"
install.packages("estimate", repos=rforge, dependencies=TRUE)Disclaimer
This website is for educational and research purposes only.