| Zilin Li

R Packages

SCANG is an R-package for performing dynamic window analysis to detect rare variant association across the genome.
SCANG boosts rare variants analysis power in the non-coding region by dynamically detecting the sizes and locations of signal regions.
SCANG controls the genome-wide type I error rate.
SCANG is computationally scalable for large-scale whole-genome sequencing studies.
The R package implementing SCANG is freely available to academic users. A manual provides instructions to the use of this package.

STAAR is an R-package for variant-set test using annotation information.
STAAR boosts rare variant association analysis power by dynamically incorporating multiple functional annotations.
STAAR is computationally scalable for large-scale whole-genome sequencing studies.
The R package implementing STAAR is freely available to academic users. A manual provides instructions to the use of this package.

STAARpipeline is an R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies.
STAARpipeline provides a streamlined rare variant association-detection framework for WGS data, including gene-centric analysis and non-gene-centric analysis using a variety of noncoding masks, conditional analysis to identify variant set signals independent of nearby common variants, and visualization of analysis results.
STAARpipeline provides five functional categories in gene-centric coding analysis.
STAARpipeline provides eight fucntional categories in gene-centric noncoding analysis.
STAARpipeline provides fixed-size sliding window analysis and data-adaptive-size dynamic window analysis in non-gene-centric analysis.
STAARpipeline automatically define and selecte all variant sets in gene-centric and non-gene-centric analysis.
The R package implementing STAARpipeline is freely available to academic users. A manual provides instructions to the use of this package. A tutorial provides a detailed example of analyzing sequencing data using STAARpipeline.

MetaSTAAR is an R package for performing rare variant meta-analysis of whole-genome/whole-exome sequencing (WGS/WES) studies.
MetaSTAAR is a powerful and resource-efficient rare variant meta-analysis framework scalable to large samples with WGS/WES and hundreds of millions of RVs across the genome.
MetaSTAAR allows for incorporating functional annotations through the STAAR framework.
The R package implementing MetaSTAAR is freely available to academic users. A manual provides instructions to the use of this package.

Web interface for multiple individual and integrative variant functional annotations of all variants across the genome.
http://favor.genohub.org/

Web interface to visualize COVID-19’s Effective Reproduction Number (Rt) in real time throughout the world, at various resolutions from country level to state/province and county levels.
http://metrics.covid19-analysis.org/