BitPhylogeny statistics

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Associated diseases

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BitPhylogeny specifications

Information


Unique identifier OMICS_12088
Name BitPhylogeny
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
Numpy, Scipy, SciKit-learn, rpy2, Pandas, h5py, Python-igraph, rPython, mcclust, e1071, igraph, gplots, riverplot, plyr
Maintained Yes

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Maintainer


  • person_outline Niko Beerenwinkel <>

Publication for BitPhylogeny

BitPhylogeny in publications

 (2)
PMCID: 5469877
PMID: 28659971
DOI: 10.3389/fgene.2017.00083

[…] uses a network to represent vafs constraints imposed by the evolutionary process. it then identifies an evolutionary model by looking for the spanning tree that best supports the cluster vaf data. bitphylogeny (yuan et al., ) provides a probabilistic framework that allows the joint inference of the number and composition of clones in a tumor, as well as the most probable tree representing […]

PMCID: 5813714
PMID: 28193548
DOI: 10.1016/j.bbcan.2017.02.001

[…] related mutations in the 58 single cells of , for example, the empirical bayes estimate of the prior tree structure is highly linear while the resulting minimum spanning tree is rather branched., bitphylogeny  works on the sample tree representation, but rather than using the single cells as leaves they are clustered together into clones. since the number of clones and their composition […]


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BitPhylogeny institution(s)
University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland

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