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@computational-epigenetics-section Waterland Lab Computational Epigenetics

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    16 repositories

    • CoRSIV-text-mining

      Public
      Repository containing code and analyses for the paper "Human systemic epigenetic variants are implicated in neurodevelopmental and metabolic disorders".
      Python
      •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • bisulfite-seq-data-analysis-pipeline

      Public
      This repo contains details of Bisulfite Processing Pipeline
      HTML
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Mar 3, 2025Mar 3, 2025

    • EWAS-analysis-permutation-testing

      Public
      This is a suite which enables to calculate the enrichment ratios of 100,000 permuted sets of CoRSIVs and control probes.
      Python
      •0•0•0•0•Updated Feb 13, 2025Feb 13, 2025

    • CoRSIV-Illumina-Overlap

      Public
      Deposits the results showing how different platforms of Illumina probes (HM450, EPIC, MSA) overlap with different versions of CoRSIV-like regions (ESS, SIV, CoR…
      Jupyter Notebook
      •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • https_share

      Public
      USCS Visualization
      0•0•0•0•Updated Jul 7, 2023Jul 7, 2023

    • CoRSIV-Capture-Design

      Public
      0•0•0•0•Updated Aug 18, 2020Aug 18, 2020

    • gbrowser_files

      Public
      0•0•0•0•Updated Feb 12, 2020Feb 12, 2020

    • CpGMatrixPlotter

      Public
      package to plot CpG matrix data as circles spaces proportionally apart
      Jupyter Notebook
      •1•1•0•0•Updated Oct 28, 2019Oct 28, 2019

    • MCCS_ESS_Cancer

      Public
      Exploratory analysis of MCCS Cancer Cohort with ESS-SIV probes
      Jupyter Notebook
      •0•0•0•0•Updated Feb 12, 2019Feb 12, 2019

    • LingyinLabNoteBook

      Public
      R
      •0•0•0•0•Updated Oct 29, 2018Oct 29, 2018

    • CX-Bin

      Public
      Used to filter and bin data generated by the bismark_methylation_extractor when running with the -CX flag
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 1, 2017Nov 1, 2017

    • M-bias-plotting

      Public
      Takes M-bias report files from bismark methylation extractor and generates plots
      Python
      •0•0•0•0•Updated Oct 18, 2017Oct 18, 2017

    • SplitByChromosome

      Public
      Python wrapper for samtools which will split a BAM file into standard chromosomes in parallel
      Python
      •0•0•2•0•Updated Oct 10, 2017Oct 10, 2017

    • BS_Capture_analysis

      Public
      Preprocessing for high resolution quality assesment
      Jupyter Notebook
      •0•0•0•0•Updated Oct 4, 2017Oct 4, 2017

    • SNP_calling

      Public
      SNP calling pipline
      Jupyter Notebook
      •0•2•0•0•Updated Sep 27, 2017Sep 27, 2017

    • Journal_club_notes

      Public
      Questions and Clarifications addressed during the Journal Club meetings will be updated here. Please create a directory for paper discussed in the Journal Club
      MIT License
      •0•0•0•0•Updated Sep 25, 2017Sep 25, 2017
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