1. CUP-AI-Dx: a deep-learning tool to infer a tumor's primary tissue of origin from its transcriptional signature. (https://github.com/TheJacksonLaboratory/CUP-AI-Dx)

  2. ChIA-PIPE: a ENCODE ChIA-PET data pipeline for comprehensive analysis and visualization. (https://github.com/TheJacksonLaboratory/chia_pipe)

  3. SCI: a python package to detect 3D genome sub-compartments from HiC data.(https://github.com/TheJacksonLaboratory/sci and  https://github.com/TheJacksonLaboratory/sci-DNN)

  4. Epihet: a Bioconductor R package to assess intra-tumor epigenetic heterogeneity burden. (http://bioconductor.org/packages/devel/bioc/html/epihet.html)

  5. R-make: a distributed analysis pipeline that processes RNA sequencing reads (http://physiology.med.cornell.edu/faculty/mason/lab/r-make/index.html)

  6. methclone: a C++ program for epigenetic clonal shift analysis using bisulfite conversion sequencing data. (https://code.google.com/p/methclone/)

  7. edmr: a R package for comprehensive DMR analysis based on bimodal normal distribution model and cost function for regional methylation analysis optimization. (https://github.com/ShengLi/edmr)

  8. methylkit: a comprehensive R package for the analysis of genome-wide DNA methylation and epigenetic sequencing profiles. (http://code.google.com/p/methylkit/)