Scientific Computer Software

The following is a selected list of software I have developed & co-developed over the years, in the fields of statistics, statistical genetics and computational biology. Most of them are on github.

Year Program Description
2017 mashr Multivariate Adaptive Shrinkage in R
2016 PFA An R package for paired factor model
2016 DSC Dynamic Statistical Comparisons
2016 SoS Script of Scripts
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 Package An R package implementing the KBAC statistic for rare variant association test
  • I maintain the Rockefeller list, a list of genetics analysis software first created in 1995. I welcome community contributions!
  • Here is a list of non-genetics software I find useful or fun.
  • Here is a list of other utility software I wrote or have edited, mostly random & dumb graduate school time killer yet some were useful at that time.