Scientific Computer Software
300 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 over the years, 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 | mmbr | 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 |
| 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 |
Software for production
- I developed the
jnbinderprogram to build research project sites.
Software lists
- 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.