|Description||A tool for predicting tumor purity, and the presence of infiltrating stromal/immune cells in tumor tissues using gene expression data.|
|Language||R (package), DHTML (website)|
|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
|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|
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.
Login is not required — it is free for anyone to use.
In early October 2016, the ESTIMATE R package was migrated to R-Forge, available here.
library(utils) rforge <- "http://r-forge.r-project.org" install.packages("estimate", repos=rforge, dependencies=TRUE)
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.
This website is for educational and research purposes only.