Here is a list of software I developed.

R CRAN/Bioconductor packages

  • ChIPComp
    differential protein binding/histone modification analysis for ChIP-seq data
  • traseR
    disease/traits enrichment analyses of trait-associated SNPs
  • glmgraph
    network/tree-based penalized regression method

github software packages

  • glmmTree
    predictive modeling of microbiome data using a phylogenetic tree-based GLMM
  • SICS
    predictive modeling of microbiome data using a phylogeny-constrained regularization for sparse GLM
  • GMPR
    normalizing zero-inflated count data particularly microbiome sequencing data
  • BAMMSC
    bayesian mixture model for clustering droplet-based scRNA-seq data from population studies
  • circMeta
    genomic feature annotation and differential expression analysis of circular RNAs
  • tfLDA
    topic models to multiple ChIP-Seq datasets to decipher the combinatorial binding of TFs
  • powmic
    power assessment in microbiome case-control studies
  • MDeep
    predictive modeling of microbiome data using a novel convolutional neural network

Database

  • hmChIP
    genome-wide ChIP-seq data in human and mouse
  • DIVAN
    disease-specific noncoding variant annotation and prioritization
  • TIVAN
    tissue-specific cis-eQTL variants annotation and prioritization