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

R CRAN/Bioconductor packages

  • ChIPComp :differential protein binding/histone modification analysis for ChIP-seq data.

  • traseR(TRait-Associated SNP EnRichment analysis) :disease/traits enrichment analyses of trait-associated SNPs in arbitrary genomic intervals.

  • glmgraph(GRAPH-constrained regularization for sparse Generalized Linear Models) :network/tree-based penalized regression method. This method could be useful in high-dimensional, sparse data prediction when the gragh/network structure among predictors are known.


github software packages

  • glmmTree :an R package for predictive modeling of microbiome data using a phylogenetic tree-based generalized mixed effects model

  • SICS :an R package for predictive modeling of microbiome data using a phylogeny-constrained regularization for sparse generalized linear models with encouraging local smoothing

  • GMPR :an R package for normalizing zero-inflated count data particular microbiome sequencing data

  • BAMMSC :an R package for a bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies

  • circMeta :an R package for genomic feature annotation and differential expression analysis of circular RNAs


Database

  • hmChIP :a database of genome-wide ChIP-seq data in human and mouse.

  • DIVAN :a database/pipeline for disease-specific noncoding variant annotation and prioritization.

  • TIVAN :a database/pipeline for tissue-specific cis-eQTL variants annotation and prioritization.