BitPhylogeny - A probabilistic framework for reconstructing intra-tumor phylogenies

BitPhylogeny

BitPhylogeny is a probabilistic framework to reconstruct intra-tumor evolutionary pathways. Using a full Bayesian approach, we jointly estimate the number and composition of clones in the sample as well as the most likely tree connecting them.

Presentations:

Download and Installation

You can download BitPhylogeny from https://bitbucket.org/ke_yuan/bitphylogeny

Requirements:

Installation:

References:

Python

Developers

Download

You can download BitPhylogeny from bitbucket.org

bitbucket

Other packages

Software
  • BaalChIP - allele-specific TF binding
  • BitPhylogeny - infer intra-tumor phylogenies
  • CRImage - tumor image analysis
  • DANCE - subtype specific drivers of cancer
  • GoIFISH - single cell IFISH analysis
  • HTSanalyzeR - functional annotation
  • lol - lots of lassos
  • MEDICC - intra-patient copy number comparison
  • nem - nested effects models
  • OncoNEM - oncogenetic NEMs
  • PAN - posterior associa- tion networks
  • RedeR - graph visualiza- tion and analysis
  • RTN - network recon- struction and analysis
  • SANTA - spatial analysis of network associations
  • VULCAN - co-factors from CHiP-seq data
Data @ Bioconductor