Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

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

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

Whole Exome/Whole Genome Sequencing alignment pipeline

Clinical Whole Genome and Exome Sequencing Pipeline

Nature Medicine paper. A Multidimensional Precision Medicine Approach for Autism Subtype Identification.

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

Workspace for data science projects and NGS pipelines. Contains RStudio, Jupyter Notebook, VSCode and file manager. Can connect to Tailscale network to bypass firewalls.

STAAR Pipeline for Analyzing Whole-Genome/Whole-Exome Sequencing Data in PheWAS (PheWAS Version of STAARpipeline)

🐳 Dockerized WES pipeline for variants identification in mathced tumor-normal samples

Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling.

LOVD+ -- LOVD for diagnostics: analysis of whole-exome data using LOVD.

Constructing Neoantigen Vaccine Pipeline with pVACtools

An app for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline in UK Biobank RAP

A lightweight R package for performing association meta-analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using MetaSTAARlite pipeline

An app for automatically functionally annotating the variants of whole-genome/whole-exome sequencing (WGS/WES) studies and integrating the functional annotations with the genotype data using FAVORannotator in UK Biobank RAP

The tutorial for performing association meta-analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, MetaSTAARlite and MetaSTAARliteSummary