genetic variant expressions, annotation, and filtering for great good.

An R package for performing STAAR procedure in whole-genome sequencing studies

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

This package scales the huge gnomAD files to a SQLite database, which is easy and fast to query. It extracts from a gnomAD vcf the minor allele frequency for each variant.

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary

An R package for performing MetaSTAAR procedure in whole-genome sequencing studies

MultiSKAT is an R-package focused at rare-variant analysis of continuous multiple phenotype data. This project contains the R-codes/functions (including an example dataset) to carry out the MultiSKAT tests.

An R package for summarizing and visualizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies generated by STAARpipeline

A collection of scripts for filtering annotated variant call format files

An R package for performing MultiSTAAR procedure in whole-genome sequencing studies

Indonesia Exome Rare Disease Variant Discovery Pipeline. Phenotype analysis part available on Streamlit and PyPi

Discover VNTR-associated DELs that are hard to find using Illumina reads

Collapsed Haplotype Pattern Method for Linkage Analysis of Next-Generation Sequencing Data

R package for the prioritization of functional rare genetic variants by integrating genomic annotations and RNA-seq

A Simple Tutorial for Analyzing Data Using the R Language

Pythonic version of RareComb

Code to use RetroFun-RVS

Mixed effects Score Test

Repository to explain the projects currently being developed at Foundation29.

RNA-seq for rare diseases pipeline using nextflow