Subcloneseeker specifications

Information


Unique identifier OMICS_08807
Name Subcloneseeker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Yi Qiao <>

Publication for Subcloneseeker

Subcloneseeker in publications

 (3)
PMCID: 5666005
PMID: 29093439
DOI: 10.1038/s41467-017-01174-3

[…] #4).fig. 1, subclonal evolution of four breast cancers was determined with 60 × whole-genome sequencing (wgs), 100 × whole-exome sequencing (wes) and targeted single-cell dna sequencing, along with subcloneseeker analysis. variants identified were validated by detection in rna-seq data (supplementary fig. ), single-nucleotide polymorphism (snp) array (supplementary fig. ), and matched clinical […]

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

[…] this strategy and their key features are given in .table 2, the methods chat  and clonehd  estimate cellular prevalences of both snvs and cnas but do not set them into a phylogenetic context. subcloneseeker infers trees based on cellular prevalences of both snv and cna data . however it relies on other tools to accurately estimate these prevalences in a preprocessing step […]

PMCID: 4318437
PMID: 25315058
DOI: 10.1186/s13059-014-0464-5

[…] that the need for a new toolkit is huge., therefore it should be no surprise that in this special issue we found a place for several excellent method articles: gabor marth and colleagues describe subcloneseeker (the clue is in the name!) [] and francesca demichelis and colleagues give us clonet [], both of which are designed for the analysis of clonality. shirley liu and colleagues [] […]


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Subcloneseeker institution(s)
Department of Biology, Boston College, Chestnut Hill, MA, USA; Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA, USA; Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Virginia Health System, Charlottesville, VA, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Huston, TX, USA; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Huston, TX, USA; Department of Human Genetics and USTAR Center for Genetic Discovery, Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
Subcloneseeker funding source(s)
This work was supported by the Fund for Excellence in Science and Technology award from the University of Virginia, by the University of Virginia’s Cancer Center (Marty Whitlow Fund); the Department of Obstetrics & Gynecology, and the by the National Human Genome Research Institute/National Institutes of Health (grants R01HG004719 and U01HG006513).

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