Tumor subclone structure reconstruction across multiple samples
Clonal heterogeneity is a defining feature of many tumor types. The elucidation of the subclones that exist within tumor samples, 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 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. When multiple tumor samples are aquired from the same patient, either via longidutinal sampling over time, or rapid autopsy approach across many metastasis sites, it is important to perform multi-sample joint subclone reconstruction to understand the overall evolution history of subclones across these samples. SuperSeeker is updated to allow for this particular function
Please refer to the documentation for how to get started, or run examples.
http://yiq.github.io/SubcloneSeekerDoc/ (currently on v1, pending update for v2)
'src' directory contains source code for the core functions of SuperSeeker in which the basic data types and logics to reconstruct super trees are defined.
'contrib' directory contains third part libraries that the project uses.
SubcloneSeeker is distributed under MIT license.
The MIT License (MIT)
Copyright (c) 2021 Yi Qiao
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