|
Assistant Professor of Research Division of Biostatistics Department of Preventive Medicine Keck School of Medicine University of Southern California 1450 East Biggy Street NRT 1450, Mailcode: 9603 Los Angeles, CA 90033 e-mail: gary.k.chen 'at' usc.edu office: (323) 442-7921 mobile: (714) 928-2705 |
|
Software
Mendel with inversions
Ken Lange's popular genetic analysis program Mendel 6.0, with multipoint linkage analysis adapted to support genomic inversions. This version also computes the posterior probability that an individual has an inversion when cytogenetic data is unavailable. A Fortran90 binary is available, compiled for 64-bit Linux.
Documentation is found here. Since Mendel has evolved since our version for inversion support, some newer file formats may not be supported, so please use the example files included in this distribution as a guide. These files are the same ones used for our paper's example. For more information on the algorithm, please refer to our manuscript.
Markovian Coalescent Simulator
MaCS is a simulator of the coalescent process that simulates geneologies spatially across chromosomes as a Markovian process. The algorithm is similar to the SMC algorithm (McVean and Cardin, Phil Trans Soc R B 2005) in that the algorithm scales linearly in time with respect to sample size and sequence length. However, it more accurately models the true coalescent, while supporting all demographic scenarios found in the popular program MS (Hudson, Bioinformatics 2002) making this program appropriate for simulating data for structured populations in genome wide association studies. Our manucript can be found here.
To install, please download the gzipped tar file
Requirements
Reversible jump MCMC sampler for Bayesian variable selection
We have recently implemented a novel variable selection method that rapidly samples the posterior distribution to explore main effects and/or higher order interactions. For more info please check out the paper here. Our method empirically weight priors on each variable (e.g. SNP, environmental covariate, interaction, etc) based on the data. The software can be downloaded here.