Software

I maintain several packages for R and Python related to analysing genetic data.

• ibdpainting: A tool to visually validate the ancestry of an individual by comparing SNP data to a panel of candidate parents. Have a look at:
  • The Github repo
  • A snakemake pipeline implementing it.
  • Examples of some of the patterns you might see.
• psiotropy: An R package for quantifying pleiotropy (the extent to which genes affect multiple traits).
  • Preprint explaining the method.
  • GitHub repo
• methlab: A Python package meant to automate common tasks related to handling bisulphite sequence data. Have a look at:
  • The GitHub repo.
  • The documentation.
• Fractional Analysis of Sibships and Paternity (FAPS): a Python package to jointly infer paternal and sibling relationships using for large SNP datasets. See the:
  • Accompanying paper with the details.
  • GitHub repo
  • Documentation, which includes extensive tutorials
• arghqtl: Tools for plotting and downstream analysis of R/QTL objects in R. It is intended in particular for cases where there are many QTL models to compare, and one’s first thought about how to plot them is ‘AAAAARGH!’.