Software

BLAZE : software for identifying cell barcodes from long-reads single-cell RNA-seq data.

Y. You*, Y.D.J. Prawer*, R. De Paoli-Iseppi, C.P.J. Hunt, C.L. Parish, H. Shim#, M.B. Clark#, Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE (*: equal contribution; #: joint corresponding authors), Genome Biology, 2023

NanoSplicer : software for accurately identifying splice junctions using Oxford Nanopore sequencing data.

Y. You, M. B. Clark#, H. Shim#, NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing (#: joint corresponding authors), Bioinformatics, 2022

McSplicer : software for estimating splice site usages using short-reads RNA-seq data.

I. Alqassem, Y. Sonthalia, E. Klitzke, H. Shim#, S. Canzar#, McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data (#: joint corresponding authors), Bioinformatics, 2021

multiseq : R package for Bayesian multi-scale models for Poisson processes.

H. Shim, Z. Xing, E. Pantaleo, F. Luca, R. Pique-Regi, M. Stephens, Multi-scale Poisson process approaches for differential expression analysis of high-throughput sequencing data, AOAS, 2024

WaveQTL : software 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, AOAS, 2015

mvBIMBAM : software 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 : software for Bayesian Co-estimation of Alignment and Tree.

H. Shim and B. Larget, BayesCAT: Bayesian Co-estimation of Alignment and Tree, Biometrics, 2017