An Efficient Swiss Army Knife for Population Genomic Analyses in R

Basic and fast GWAS functions for QQ and Manhattan plots (incl. gene names)

visual analysis of your VCF files

metaUSAT is a data-adaptive statistical approach for testing genetic associations of multiple traits from single/multiple studies using univariate GWAS summary statistics.

Statistical and computational analysis of the human genome

Handy reusable bioinformatic scripts

An integrated pipeline for analysis and visualization of Population Structure and Relatedness based on genome-wide genetic variant data

Pipeline to identify repetitive elements on non-model species genomes.

mvtests: a suite of functions for testing genetic associations of multiple traits (a.k.a. cross-phenotype associations)

USAT uses a data-adaptive weighted score-based test statistic for testing association of multiple continuous phenotypes with a single genetic marker.

Software supporting M. Cavallaro, et al., 3′-5′ crosstalk contributes to transcriptional bursting. Genome Biol 22, 56 (2021). https://doi.org/10.1186/s13059-020-02227-5

Genome Analysis Toolkit

A human-first SV annotation snakemake pipeline based on nanotatoR working with optical mapping (Bionano Genomics) data

Create a Bioconductor/R SDK for Arvados

Analysis of input alphabet sequential data

Optimal AlphaMissense threshold based on VKGL variant classifications

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

POM-PS tests for genetic associations of secondary traits from case-control GWAS.