Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: PairClone: A Bayesian Subclone Caller Based on Mutation Pairs   Tumor cell populations can be thought of as being composed of homogeneous
cell subpopulations, with each subpopulation being characterized by overlapping
sets of single nucleotide variants (SNVs). Such subpopulations are known as
subclones and are an important target for precision medicine. Reconstructing
such subclones from next-generation sequencing (NGS) data is one of the major
challenges in precision medicine. We present PairClone as a new tool to
implement this reconstruction. The main idea of PairClone is to model short
reads mapped to pairs of proximal SNVs. In contrast, most existing methods use
only marginal reads for unpaired SNVs. Using Bayesian nonparametric models, we
estimate posterior probabilities of the number, genotypes and population
frequencies of subclones in one or more tumor sample. We use the categorical
Indian buffet process (cIBP) as a prior probability model for subclones that
are represented as vectors of categorical matrices that record the
corresponding sets of mutation pairs. Performance of PairClone is assessed
using simulated and real datasets. An open source software package can be
obtained at http://www.compgenome.org/pairclone.

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The categories of this paper are: hep-ph
30
The categories of this paper are: q-alg
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The categories of this paper are: quant-ph
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The categories of this paper are: hep-th
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The categories of this paper are: dg-ga
25
The categories of this paper are: patt-sol
10
The categories of this paper are: q-bio
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The categories of this paper are: nucl-ex
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The categories of this paper are: supr-con
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The categories of this paper are: gr-qc
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The categories of this paper are: math-ph
33
The categories of this paper are: plasm-ph
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The categories of this paper are: chem-ph
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The categories of this paper are: nlin
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The categories of this paper are: cond-mat
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The categories of this paper are: atom-ph