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Estimation of STromal and Immune cells in MAlignant Tumors using Expression data ESTIMATE

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Uses gene expression signature to infer the fraction of stromal and immune cells in tumor tissues. ESTIMATE scores correlate with DNA copy number-based tumour purity across samples from 11 different tumour types, profiled on Agilent, Affymetrix platforms or based on RNA sequencing and available through The Cancer Genome Atlas. The prediction accuracy is further corroborated using 3,809 transcriptional profiles available elsewhere in the public domain. The ESTIMATE method allows consideration of tumour-associated normal cells in genomic and transcriptomic studies.

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ESTIMATE forum

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ESTIMATE versioning

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ESTIMATE classification

ESTIMATE specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Source code URL:
https://sourceforge.net/p/estimateproject/code/ref/master/
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Version:
1.0.13
Maintained:
Yes

ESTIMATE support

Documentation

Maintainer

  • Roel Verhaak <>

Credits

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Publications

Institution(s)

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Centre, Houston, TX, USA; Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan; Department of Systems Biology, The University of Texas MD Anderson Cancer Centre, Houston, TX, USA; Catedra de Bioinformatica, Tecnologico de Monterrey, Campus Monterrey, Monterrey, Nuevo Leon, Mexico; USC Epigenome Centre, University of Southern California, Los Angeles, CA, USA; Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Centre, New York, NY, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA

Funding source(s)

This work was supported by the U.S. National Cancer Institute (grant n°CA143883 to The University of Texas MD Anderson Genome Data Analysis Centre).

Link to literature

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