# 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 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 | 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

- The
`jnbinder`

program to build research project sites. - Genetic fine-mapping with summary statistics.
- Multivariate adaptive shrinkage analysis see usage here.

### Dynamic Statistical Comparisons

- Genetic fine-mapping methods.
- Large scale regression.
- Differential expression analysis for single cell RNA-seq data.

## Software lists

- 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.