Computational Framework to reconstructing tumor clone structures
Clonal heterogeneity is a defining feature of many tumor types, and the elucidation of the subclones that exist within the tumor sample, together with the corresponding cellular fractions, is essential to understand tumorigenesis, relapse, and metastasis. We developed a software framework, SubcloneSeeker, that examines somatic variation events (such as copy number changes, loss of heterozygosity, or point mutations) in order to identify the underlying subclone structure, i.e. the subclones including the normal (non-cancerous) cells and their cellular frequencies within the tumor tissue.
Please refer to the documentation for how to get started, or run examples.
'src' directory contains all the classes that consists of the SubcloneSeeker core library, in which the basic data types and logics for representing somatic mutations, mutation clusters and subclones are defined.
'utils' directory contains the source code for many command-line utilities that utilizing the SubcloneSeeker core library.
'test' directory contains the test cases for the core library.
'doc' directory contains the project's documentation, generated by Doxygen. A pre-built version can be read at http://yiq.github.io/SubcloneSeekerDoc/
'contrib' directory contains third part libraries that the project uses.
SubcloneSeeker is distributed under MIT license.
The MIT License (MIT)
Copyright (c) 2013 Yi Qiao
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.