PurBayes statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool PurBayes
info

Tool usage distribution map

This map represents all the scientific publications referring to PurBayes per scientific context
info info

Associated diseases

info

Popular tool citations

chevron_left Tumor purity and heterogeneity estimation chevron_right
Want to access the full stats & trends on this tool?

PurBayes specifications

Information


Unique identifier OMICS_03561
Name PurBayes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The tumor tissue read counts (N and Y) for a set of high-confidence SNVs.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.3
Stability Stable
Requirements
rjags
Source code URL https://cran.r-project.org/src/contrib/PurBayes_1.3.tar.gz
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Nicholas B. Larson

Publication for PurBayes

PurBayes citations

 (4)
call_split

Characterization of genetic intratumor heterogeneity in colorectal cancer and matching patient‐derived spheroid cultures

2017
Mol Oncol
PMCID: 5748486
PMID: 29130628
DOI: 10.1002/1878-0261.12156
call_split See protocol

[…] allele frequencies (AFs) were calculated using SAMtools mpileup. Copy number alterations (CNAs) and allelic imbalance were estimated using FACETS (Shen and Seshan, ). Tumor purity was estimated using PurBayes (Larson and Fridley, ) and Sequenza (Favero et al., ). Tumor drivers and potentially druggable targets were identified using the IntOGen catalog of cancer drivers, available for download at I […]

library_books

Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy

2015
PLoS One
PMCID: 4687867
PMID: 26695660
DOI: 10.1371/journal.pone.0145176

[…] lower tumor purity compared to that of PDXs.DNA tumor purity was estimated at 75% for visit 1 and 76% for visit 2 metastatic samples using the frequency of the most frequent subclone, as computed by PurBayes. The clonality analyses indicated that all three major clones were maintained at relative stable frequencies between patient tissue and PDXs, as well as among different passages of PDXs (). […]

library_books

Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

2015
Nat Genet
PMCID: 4587544
PMID: 25822088
DOI: 10.1038/ng.3252

[…] fied according to the clinical, pathological and genetic features as previously described by Guichard et al. (, ). In all HCC samples, the ratio of tumor cells/non-tumor cells was evaluated >50%; the PurBayes method estimated an average 70% (range 39-100%) of tumor purity based upon sequencing data (). Definition of DMN, early, small and progressed, classic, and poor prognosis HCC is based on hist […]

library_books

Ploidy Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations

2015
Genome Med
PMCID: 4343275
PMID: 25729435
DOI: 10.1186/s13073-015-0127-5

[…] SciClone [] and PurBayes [] were applied to mixed BAM files at varying coverage depths (30X, 50X, 100X) to estimate clonal subpopulations using the mutation frequency data and copy number profiles. SciClone is an R p […]


Want to access the full list of citations?
PurBayes institution(s)
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA; Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
PurBayes funding source(s)
Supported by the Mayo Foundation and the US National Institute of Health (R21 GM86689; P30 CA168524; P20 GM103418).

PurBayes review

star_border star_border star_border star_border star_border
star star star star star
Calvi. C.'s avatar image

Calvi. C.

star_border star_border star_border star_border star_border
star star star star star
Desktop
Great, works.