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 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.
|2019||MIRAGE||An R package for mixture model based rare variant association analysis|
|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: 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.
jnbinderprogram to build research project sites.
- Genetic fine-mapping with summary statistics.
- Multivariate adaptive shrinkage analysis see usage here.
- WGS genotype calling via
Dynamic Statistical Comparisons
- Genetic fine-mapping methods.
- Large scale regression.
- Differential expression analysis for single cell RNA-seq data.
Please find here the list of pipelines developed from my group.
- I am the current maintainer the Rockefeller list (after Dr. Wentian Li and Dr. Jurg Ott), a list of genetics analysis software first created in 1995.
- 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.