# 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

- 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.