OncoNEM - Inferring tumour evolution from single-cell sequencing data

OncoNEM

OncoNEM is a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells.

OncoNEM identifies homogeneous cellular subpopulations and infers their genotypes as well as a tree describing their evolutionary relationships.


Download and Installation

You can download OncoNEM from https://bitbucket.org/edith_ross/onconem

To install this package directly in R type:

  library(devtools)
  install_bitbucket("edith_ross/oncoNEM")
  

Reference:

R

Developers

Download

You can download OncoNEM 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