These are published software that I have developed. For a complete list, including work in progress, please see https://github.com/PeteHaitch. I also contribute to the bsseq Bioconductor package and more broadly to the Bioconductor project.
methtuple: methtuple is a methylation caller for methylation events that co-occur on the same DNA fragment from high-throughput bisulfite sequencing data, such as methylC-seq.
GenomicTuples: GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.
XGWAS: R code for paper: Hickey, P. F., & Bahlo, M. (2011). X chromosome association testing in genome wide association studies. Genetic Epidemiology, 35(7), 664–670. doi:10.1002/gepi.20616