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    17 repositories

    • Analysis-Example-Codes

      Public
      R scripts from Ze Zhang often used in DNA methylation analyses. Not the most clean but should be helpful
      R
      •2•0•0•0•Updated Dec 22, 2023Dec 22, 2023

    • MethylCapsNet

      Public
      Python
      •
      MIT License
      •2•4•3•0•Updated Mar 26, 2021Mar 26, 2021

    • methyl_capsule_data

      Public
      Stores data for capsule-related projects
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Nov 9, 2020Nov 9, 2020

    • PCNS_5hmC_06112020

      Public
      Measurement of 5hmC in pediatric cns tumors
      R
      •1•1•0•0•Updated Jun 11, 2020Jun 11, 2020

    • MethylNet

      Public
      Modular framework for deep learning predictions on methylation data.
      HTML
      •
      MIT License
      •11•51•6•0•Updated Jun 2, 2020Jun 2, 2020

    • PyMethylProcess

      Public
      Preprocessing methylation pipeline, written in python. Easy to use and highly parallelized.
      Python
      •
      MIT License
      •8•35•9•0•Updated Feb 11, 2020Feb 11, 2020

    • Normal-breast-5hmC

      Public
      HTML
      •1•3•0•0•Updated Nov 19, 2019Nov 19, 2019

    • VAE_methylation

      Public
      VAE methylation analysis using the Tybalt model developed by Way et al.
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •2•9•0•0•Updated May 31, 2019May 31, 2019

    • VAE_analysis

      Public
      DNA methylation analysis using VAE
      Jupyter Notebook
      •1•5•0•0•Updated Nov 6, 2018Nov 6, 2018

    • CF_Epigenetics

      Public
      R code repository for statistical analysis and data visualization of manuscript "Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with Lung Macrophages in cystic fibrosis"
      R
      •
      GNU General Public License v3.0
      •3•8•0•0•Updated Sep 21, 2018Sep 21, 2018

    • HNSCC-miRSNP-Survival

      Public
      R
      •1•2•0•0•Updated Sep 19, 2018Sep 19, 2018

    • Lab-Tutorials

      Public
      Programming tutorials for the Christensen Lab
      R
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Aug 4, 2018Aug 4, 2018

    • shared_450K_annotation

      Public
      R
      •0•2•1•0•Updated Apr 19, 2018Apr 19, 2018

    • brca_lowstage_DMGRs

      Public
      The repository stores the analytical code for the pre-release of the manuscript titled "Tumor subtype and cell type independent DNA methylation alternations reveals twelve genes associated with low stage breast carcinoma".
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •3•4•0•0•Updated Sep 14, 2017Sep 14, 2017

    • Normal-Breast-Methylation

      Public
      R
      •0•8•0•0•Updated Jul 10, 2017Jul 10, 2017

    • OxyBS

      Public
      Vignette for data processing and use of the fitOxBS function from the OxyBS R package
      R
      •2•3•0•0•Updated Mar 16, 2016Mar 16, 2016

    • methyLiftover

      Public
      A utility to map bisulfite sequencing data to the Illumina 450K methylation CpG set
      R
      •14•17•3•0•Updated Feb 12, 2016Feb 12, 2016