Software

I have bits of software related to my work available on my github. Some highlights are provided below

Single cell genomics

I have an R package to estimate allele specific copy number in single cells available here. This also includes lots of functionality to analyse single cell genomes.

Software used in publications

Quantification of subclonal selection in cancer from bulk sequencing data

See here for a post detailing some of the software I developed for this paper.

Identification of neutral tumour evolution across cancer types

In this paper we showed that sequencing data from a large proportion of cancers fitted a neutral evolution model. As part of this work we used a simulation of cancer evolution. A jupyter notebook showing the results of the simulation is available here.