Here is a list of software packages I developed or co-developed.

Bioconductor packages

  • DSS (Dispersion Shrinakge for Sequencing): differential analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq).

  • TOAST (TOols for the Analysis of heterogeneouS Tissues): designed for the analyses of high-throughput data from heterogeneous tissues that are mixtures of different cell types. TOAST offers functions for detecting cell-type specific differential expression (csDE) or differential methylation (csDM), as well as improved reference-free deconvolution for mixing proportion estimation.

  • PROPER (PROspective Power Evaluation for RNAseq): simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.

  • ChIPComp: Differntial protein binding analysis for ChIP-seq data. The package can potentially be used for differntial analyses from other capture sequencing data with controls such as m6A capture or Ribo-seq data.
  • maanova: Differntial expression analysis of N-dye microarray experiments using mixed model effect.

Other non-bioconductor software

  • JAMIE (Joint Analysis of Multiple IP Experiments).
  • makeCGI: finding [CpG islands] ( (CGIs) from DNA sequences.
  • R/qtl: mapping quantitative trait loci (QTL) in experimental crosses.
  • J/qtl: a Java graphical user interface (GUI) for R/qtl.