I develop and maintain freely-available, open-source software packages in R/Bioconductor/CRAN/GitHub to analyze high-throughput genomics data. They are available through R cran, Bioconductor or GitHub.

  • DSS Usage Stats
    (Dispersion Shrinakge for Sequencing): differential analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated regions (DMRs) from bisulfite sequencing (BS-seq) data. Available on Bioconductor.

  • NeuCA Usage Stats
    (Neural-network based Cell type Annotation): R/Bioconductor package for single-cell RNA-seq data cell type annotation, using neural-network approaches. NeuCA is flexible and adjust the classification method it will adopt, depending on cell types’ correlation level. Currently available on Bioconductor.

    ISLET (Individual-Specific ceLl typE referencing Tool) can deconvolute mixture samples and obtain the individual-specific and cell-type-specific reference panels. Available on GitHub. In submission to Bioconductor.

  • InfiniumPurify
    R CRAN package for the estimation and adjustment for tumor purity in cancer methylation data analysis, available on R CRAN.

  • cfDNAmethy
    Reference-free and reference-based models for disease prediction by cell-free DNA methylation, available on GitHub.