Scientific Computer Software

400 Words | Approximately 2 Minutes Read | Last Modified on January 22, 2019

Companion software for journal publications

The following is a selected collection of software I have developed & co-developed during my PhD and postdoc trainings, in the fields of statistics, statistical genetics and computational biology. Most of them are on github and are companion to peer reviewed journal papers.

Year Program Description
2019 MIRAGE An R package for mixture model based rare variant association analysis
2019 mvsusieR Multivariate Bayesian variable selection using adaptive shrinkage methods
2018 susieR Sum of single effect model for large scale Bayesian regression
2017-2018 mashr Multivariate Adaptive Shrinkage in R
2016-2018 PFA An R package for paired factor model
2016-2018 DSC Dynamic Statistical Comparisons
2016-2018 SoS Script of Scripts: a simple yet powerful bioinformatics workflow system
2015 eQtlBma Joint eQTL analysis for large number of subgroups via Bayesian model averaging
2013-2014 SEQLinkage A method to perform Linkage analysis using next-generation sequence data
2013-2014 RarePedSim Simulation of DNA sequence data of human pedigrees with complex traits
2012-2013 SEQPower Sample size and power calculation of rare variants association study designs
2012-2014 Variant Association Tools Quality control and association testing of next-generation sequence data
2012 Variant Annotation Tools Annotation and filtering of variants in human genome
2011 KBAC An R package for the KBAC rare variant association test

Pipelines & benchmarks

Below are some pipelines and benchmarks I wrote during my postdoc training at University of Chicago.

Bioinformatics workflows

Dynamic Statistical Comparisons

Software lists