Subcloneseeker statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Subcloneseeker
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Tool usage distribution map

This map represents all the scientific publications referring to Subcloneseeker per scientific context
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Associated diseases

This word cloud represents Subcloneseeker usage per disease context
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Popular tool citations

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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Yi Qiao

Publication for Subcloneseeker

Subcloneseeker citations

 (2)
call_split

Combating subclonal evolution of resistant cancer phenotypes

2017
Nat Commun
PMCID: 5666005
PMID: 29093439
DOI: 10.1038/s41467-017-01174-3
call_split See protocol

[…] tute/oncotator). CNAs were called from WES using VarScan v2.3.7 (http://dkoboldt.github.io/varscan) copynumber and copyCaller, from pileups generated by SAMTools, to determine copy-number 2 genes for SubcloneSeeker. Segmentation was done with DNAcopy in R. Segmented data were converted to gene level using UCSC’s refGene.txt (hg19) annotation. Log2 fold-change values were converted to absolute copy […]

library_books

Advances in understanding tumour evolution through single cell sequencing*

2017
Biochim Biophys Acta
PMCID: 5813714
PMID: 28193548
DOI: 10.1016/j.bbcan.2017.02.001

[…] ethods following this strategy and their key features are given in .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 and is restricted […]


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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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