Software

PeakSEA

PeakSEA is an R package to compute rank-based enrichment of genomic regions in a set of peaks. It is designed to be used with ATAC-seq, ChIP-seq, and other peak-based genomic data. The package takes advantage of the GSEA method to compute enrichment scores for a given set of pre-ranked peaks against reference peak sets of interest (e.g. conserved regions, GWAS loci), allowing users to identify genomic regions that are significantly enriched in their data.

bigQTL

bigQTL is an R package extending bigsnpr to perform fast and efficient cis-QTL mapping on genomic datasets. Its main feature is its ability to do step-wise and all-but-one conditioning efficiently across many molecular traits.

plyranges

I am a contributor to the plyranges package as part of the tidyomics consortium. plyranges is an R package that provides a grammar for manipulating genomic ranges in a tidy and consistent manner. It allows users to perform common operations on genomic ranges, such as filtering, joining, and summarizing, using the tidy syntax.