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A multitude of tools for comparative genomics, focused on large-scale analyses of biological data. SynExtend includes tools for working with syntenic data, clustering massive network structures, and estimating functional relationships among genes.

Infers maternal and paternal transmitted and non-transmitted alleles from phased trio genotype data. The package supports SNP-level analyses of genetic nurture and transgenerational effects. It interoperates with Bioconductor VCF infrastructure through support for VariantAnnotation::VCF objects and returns R objects for downstream analysis.

`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.

This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results.

Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) running locally to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.

Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins - either as provided by default parameters or estimated from target data - and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants, allele frequency spectrum, haplotype structure, and variant annotation.

Provides a framework for allelic specific expression investigation using RNA-seq data.