McSplicer : a software package that implements a probabilistic model for alternative splicing in Python
multiseq : an R package for Bayesian multi-scale models.
- H. Shim*, Z. Xing*, E. Pantaleo and M. Stephens, Bayesian multi-scale models for detecting differences in high-throughput sequencing data between multiple groups and their applications in small sample sizes, in prep.
WaveQTL : a software package for wavelet-based genetic association analyses of high-throughput sequencing data.
- H. Shim and M. Stephens, Wavelet-based genetic association analysis of functional phenotypes arising from high-throughput sequencing assays, to appear in AOAS.
mvBIMBAM : a software package for multivariate association analyses.
- H. Shim, D. I. Chasman, J. D. Smith, S. Mora, P. M. Ridker, D. A. Nickerson, R. M. Krauss, M. Stephens, A multivariate genome-wide association analysis of 10 LDLsubfractions, and their response to statin treatment, in 1868 Caucasians, PLoS ONE 10(4): e0120758, 2015.
BayesCAT : a software package for Bayesian Co-estimation of Alignment and Tree.
- H. Shim and B. Larget, BayesCAT: Bayesian Co-estimation of Alignment and Tree, under review.
SUCcESS : an R package and a stand-alone C program for integrating heterogeneous high-throughput genomic data into motif finding.
- H. Shim and S. Keles. Integrating quantitative information from ChIP-chip experiments into motif finding, Biostatistics, 9(1):51-65, 2007.
TileHGMM : an R package for mixture modeling of genome-wide localization of transcription factors.
- S. Keles. Mixture modeling for genome-wide localization of transcription factors, Biometrics, 63(1): 10-21, 2007.