MEDICC - Minimum Event Distance for Intra-tumour Copy number Comparisons

MEDICC

MEDICC harnesses the power of a finite-state automaton representation of genomic profiles to model genomic rearrangement events with horizontal dependencies.

Efficient transducer-based implementations allow for the exact computation of evolutionary distances and ancestral reconstructions.

The accompanying R package MEDICCquant implements follow-up analyses including tests for molecular clock, tests for phylogenetic structure, and quantification of clonal expansion and heterogeneity.

Download and Installation

You can download MEDICC from https://bitbucket.org/rfs/medicc

Requirements:

Installation:

References:

Python

Developers

Download

You can download MEDICC 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
Data @ Bioconductor