caravagn

CleanCNA

An R package to classify a copy number call as of high or low quality, to re-estimate purity and ploidy parameters based on a set of collected metrics, and to iteratively rerun the copy number calling process to provide a high quality set of copy number calls using WGS data.

scMET

Bayesian modelling of DNA methylation heterogeneity at single-cell resolution

rcongas

rcongas

congas

A set of Pyro models and functions to infer CNA from scRNA-seq data

myprettyreport

Custom PDF report layouts to export ggplot2 visualizations

HyperTraPS

HyperTraPS discrete time framework for inferring high-dimensional pathways of trait acquisition.

MiMMAl

Using two-component Gaussian mixture modelling to estimate the major allele distribution in genotying data.

DPClustering.jl

Dirichilet process clustering for cancer sequencing data

neutralitytestr

Testing a neutral evolution model on cancer sequencing data

SubClonalSelection.jl

Inferring selection in cancer sequencing data using ABC and population based simulations

CancerSeqSim.jl

pheatmap

Pretty heatmaps

Mixture-Models

Mixture Models - EM and Gibbs sampling

MST

MST testing

PiCnIc-COADREAD

PiCnIc implementation for COADREAD

mutex

Automatically exported from code.google.com/p/mutex

oncoprintjs

OncoPrint visualization

TRONCO

Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).