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Protocols

SciClone specifications

Information


Unique identifier OMICS_05106
Name SciClone
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Apache License version 2.0
Computer skills Advanced
Version 1.1.0
Stability Stable
Requirements
IRanges, ggplot2, sciclone
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Li Ding
  • person_outline Chris Miller

Additional information


The Genome Institute, Washington University, St. Louis, MO, USA; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University, St. Louis, MO, USA; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, USA; Massachusetts General Hospital, Boston, MA, USA; Liggins Institute, Auckland, New Zealand

Publication for SciClone

SciClone citations

 (31)
library_books

Resistance promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient

2018
PMCID: 5880262
PMID: 29440180
DOI: 10.1101/mcs.a002444

[…] acterized the heterogeneity of each tumor specimen and compared it to the others in the series. Here, copy-number-neutral variants and their attendant VAFs were clustered in five dimensions using the sciClone algorithm v1.1 () (parameters: minimumDepth = 300, maximumClusters=15), followed by phylogeny reconstruction with clonEvol (). […]

library_books

Novel mutational landscapes and expression signatures of lung squamous cell carcinoma

2017
Oncotarget
PMCID: 5800913
PMID: 29484121
DOI: 10.18632/oncotarget.23716

[…] The bioinformatics tools – SciClone [] and clonevol package (https://github.com/hdng/clonevol) were used to identify the clonal structures of each of the 16 mouse LUSC tumors. Single-cell gene mutations were analyzed using the […]

library_books

Engineered in vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer

2017
Sci Rep
PMCID: 5647443
PMID: 29044127
DOI: 10.1038/s41598-017-13338-8

[…] PyClone 0.13.0 available from http://compbio.bccrc.ca/software/pyclone.Clomial 1.3.0 available at R-bioconductor.SciClone available from https://github.com/genome/sciclone.PhyloWGS available from https://github.com/morrislab/phylowgs. […]

library_books

Simultaneous evolutionary expansion and constraint of genomic heterogeneity in multifocal lung cancer

2017
Nat Commun
PMCID: 5634994
PMID: 29018192
DOI: 10.1038/s41467-017-00963-0

[…] PyClone and SciClone were employed to detect subclones. PyClone applied an MCMC method to cluster variants. SciClone focused primarily on variants in copy number neutral, loss of heterozygosity (LOH)-free portion […]

library_books

Spatial genomic heterogeneity in multiple myeloma revealed by multi region sequencing

2017
Nat Commun
PMCID: 5559527
PMID: 28814763
DOI: 10.1038/s41467-017-00296-y

[…] C chromosomes, we assigned n chr the value of C with the maximum likelihood using a binomial distribution. The CCF was calculated by dividing n mut by n chr. Clonal substructures were inferred using SciClone with default parameters and the filtered set of SNVs. For the manual design of mock phylogenetic trees, the output of SciClone was further interpreted after inclusion of copy number data, foc […]

call_split

Mutational Landscapes of Smoking Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center

2017
Theranostics
PMCID: 5562225
PMID: 28824725
DOI: 10.7150/thno.20355
call_split See protocol

[…] ficance of mutated genes. All analyses were performed with R statistical computing software version 3.3.0 . Mutagenic processes and tumor clonality were analyzed with R packages somaticSignatures and SciClone, respectively (Supplementary Methods) . […]


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SciClone institution(s)
Supported by NHGRI grant U01HG006517, NHGRI grant U54HG003079, an International Myeloma Foundation Brian D. Novis research grant, Barnes-Jewish Hospital Foundation grant 7603-55, NIH/NCI SPORE in Leukemia grant P50CA171063, NIH/NCI grant 1K12CA167540, and Clinical and Translational Award from the NIH National Center for Advancing Translational Sciences grant UL1 TR000448.

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