Copyright 2012, 2013, 2014, 2015 Brown University, Providence, RI.
All Rights Reserved
Permission to use, copy, modify, and distribute this software and its
documentation for any purpose other than its incorporation into a
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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: layla@cs.brown.edu
braphael@cs.brown.edu
Beta Version: 0.7
Version data: October, 2015
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