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