PyClone statistics

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PyClone specifications

Information


Unique identifier OMICS_03424
Name PyClone
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.12.7
Stability Stable
Maintained Yes

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Publications for PyClone

PyClone in publications

 (40)
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] portal in day 29th of september 2017. frequencies of germline mutations in general population were retrieved from the exac database (access on 12 october 2017)., clonal evolution was inferred with pyclone. parameters used to define clusters of snvs were: (i) at least five snvs and (ii) mean cancer cell fraction of at least 10% in one sample., the whole blood was washed in pbs 1x with 0.4 g/l […]

PMCID: 5832792
PMID: 29497050
DOI: 10.1038/s41467-018-03276-y

[…] monoclonal origin of h-chc (fig. ). in addition, clonal analyses suggested common mutation clusters for all seven h-chc patients after adjusting for cancer cell fraction (ccf) for each sample using pyclone (fig. )–.fig. 5, the findings above obtained by analyzing systematic mutations, somatic cnvs, clonal analyses as well as hbv integrations all imply that h-chc originates from a common […]

PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] samples were compared in a pair-wise fashion: sample at f/u vs. sample at diagnosis. estimations of cellular prevalences and clustering of mutated populations were obtained by the bayesian framework pyclone using its own binomial density model with 10,000 mcmc iterations and default priors (shape = 1.0; rate = 0.001; initial concentration = 1.0; alpha = 1; beta = 1). as input, we only considered […]

PMCID: 5940637
PMID: 29568095
DOI: 10.1038/s41375-018-0043-y

[…] nor was it associated with a specific clinical phenotype, although this can only be addressed with a larger series.fig. 1, to understand the clonal substructure of these spatially separated tumors, pyclone[], a model-based clustering algorithm (supplementary methods) was used to derive pairwise sub(clonal) clusters and reconstruct clonal phylogenies for each case (fig.  and ). this demonstrated […]

PMCID: 5828205
PMID: 29535832
DOI: 10.18632/oncotarget.24365

[…] tumor by laser capture microdissection. next-generation sequencing was performed in each component, and the mutation profiles were compared. for further inference of phylogenies, phylogenetic and pyclone analyses were performed. mismatch repair disturbance and programmed death ligand-1 (pd-l1) expression were also evaluated., comparative genetic analysis of different histological areas […]


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PyClone institution(s)
Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Statistics, University of British Columbia, Vancouver, BC, Canada

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