PyLOH specifications

Information


Unique identifier OMICS_03559
Name PyLOH
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
Numpy, Scipy, Pysam
Maintained Yes

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Documentation


Maintainers


  • person_outline Xiaohui Xie <>
  • person_outline Yi Li <>

Publication for PyLOH

PyLOH in publications

 (2)
PMCID: 5832318
PMID: 29494651
DOI: 10.1371/journal.pone.0193689

[…] compared with corresponding acgh fold changes (r2 = 0.89; )., different bioinformatic methods are already available to determine cancer ploidy and purity such as absolute [], ascat [], theta [] and pyloh []. the first two are however designed for snp array data and do not formally model dna sequencing data, theta is designed to identify subclonal cnas in mixed samples data obtained by high […]

PMCID: 5723949
PMID: 29279850
DOI: 10.1155/2017/5482750

[…] infer phylogenies using both somatic copy number alterations and single-nucleotide alterations from one or more samples derived from a single patient. li and xie [] propose a software package called pyloh to deconvolve the mixture of normal and tumor cells using copy number alterations and loh information. yu et al. [] introduce clonecna to address normal cell contamination, tumor aneuploidy, […]


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PyLOH institution(s)
Department of Computer Science, University of California, Irvine, CA, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA; Center for Machine Learning and Intelligent Systems, University of California, Irvine, CA, USA
PyLOH funding source(s)
Supported by National Institute of Health (grant R01HG006870).

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