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  1. Nanome: DNA methylation calling pipeline for Oxford Nanopore sequencing. (https://github.com/liuyangzzu/nanome)                                                                                   

  2. 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)
     

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

  4. 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)
     

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

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

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

  8. 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)
     

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

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