Software

Shim lab github page and Heejung’s github page


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.