Software

Software Developed/co-Developed:

  • DSS: Dispersion Shrinkage for Sequencing.

An R/Bioconductor package for differential analysis from high-throughput sequencing data, including differential expression for RNA-seq and differential methylation for bisulfite-sequencing data. Available at http://www.bioconductor.org/packages/release/bioc/html/DSS.html.

  • InfiniumPurify

Our proposed method 'InfiniumClust' was integrated into 'InfiniumPurify'. It is a comprehensive R package for estimating and accounting for tumor purity based on DNA methylation Infinium 450k array data. It provides functionalities for tumor purity estimation. In addition, it can perform differential methylation detection and tumor sample clustering with the consideration of tumor purities. Available at https://cran.r-project.org/web/packages/InfiniumPurify/index.html.

  • cfDNAmethy

Reference-free and reference-based methods for disease prediction by cell-free DNA methylation. Available at https://github.com/haoharryfeng/cfDNAmethy.