An Efficient Swiss Army Knife for Population Genomic Analyses in R

visual analysis of your VCF files

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

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

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

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

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

Plastome Assembly Coverage Visualization in R

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

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

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

Analysis of input alphabet sequential data

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.

Create a Bioconductor/R SDK for Arvados

Optimal AlphaMissense threshold based on VKGL variant classifications

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