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http://cs.brown.edu/people/braphael/software.html
README file for Tumor Heterogeneity Analysis (THetA)
Software that estimates tumor purity and clonal/subclonal copy number
aberrations directly from high-throughput DNA sequencing data.
If you use this software in your research, please cite:
L. Oesper, G. Satas, B.J. Raphael. (2014) Quantifying Tumor Heterogeneity
in Whole-Genome and Whole-Exome Sequencing Data. Bioinformatics. (In Press).
L. Oesper, A. Mahmoody, B.J. Raphael. (2013) THetA: Inferring intra-tumor
heterogeneity from high-throughput DNA sequencing data. Genome Biology. 14:R80.
contact: [email protected]
[email protected]
Beta Version: 0.62
Version data: October, 2014
WEBSITE:
http://compbio.cs.brown.edu/software/
http://compbio.cs.brown.edu/projects/theta/
SUMMARY========================================================================
This software is for estimating tumor purity (fraction of non-cancerous cells)
and clonal/subclonal copy number aberrations from high-throughput DNA
sequencing data for a tumor normal pair.
CONTENTS ======================================================================
(i) Documentation (in doc/ subdirectory):
* Manual; MANUAL.txt - A complete description of how to install/run the software.
* Release Notes; RELEASE_NOTES.txt - List of changes between different versions.
* License; LICENSE.txt - The complete license that goes with the software.
(ii) Software (Main code in python/ Additional code in java/src/,
jarfiles, and matlab/ subdirectories):
* Source code in python/, java/src and matlab/
(iii) Executables (in bin/ subdirectory ):
* Executables for compiling and running code
(iv) Example (in example/ subdirectory)
* Example input/output files
(v) Data (in data/ subdirectory)
* Useful data files for use with whole-exome sequencing data