PurBayes 1.3 – Bayesian Estimation of Tumor Purity and Clonality

PurBayes 1.3

:: DESCRIPTION

PurBayes is an MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

::DEVELOPER

Fridley Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 PurBayes

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1888-9. doi: 10.1093/bioinformatics/btt293. Epub 2013 Jun 6.
PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data.
Larson NB1, Fridley BL.

CITUP v0.1.0 – Clonality Inference in Multiple Tumor Samples using Phylogeny

CITUP v0.1.0

:: DESCRIPTION

CITUP is a bioinformatics tool that can be used to infer tumor heterogeneity using multiple samples from a single patient. Given mutational frequencies for each sample, CITUP uses an optimization based algorithm to find the evolutionary tree best explaining the data.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • IBM ILOG CPLEX Optimization Studio

:: DOWNLOAD

 CITUP

:: MORE INFORMATION

Citation

Clonality Inference in Multiple Tumor Samples using Phylogeny.
Malikic S, McPherson AW, Donmez N, Sahinalp CS.
Bioinformatics. 2015 Jan 6. pii: btv003.

CLONET v2 – CLONality Estimate in Tumors

CLONET v2

:: DESCRIPTION

CLONET is a collection of R scripts which upon estimation of tumor admixture and ploidy infers the clonal hierarchy of genomic aberrations.

::DEVELOPER

Demichelis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOSX
  • R

:: DOWNLOAD

 CLONET

:: MORE INFORMATION

Citation:

Genome Biol. 2014 Aug 26;15(8):439. doi: 10.1186/s13059-014-0439-6.
Unraveling the clonal hierarchy of somatic genomic aberrations.
Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F.