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    13 repositories

    • MethylStar

      Public
      A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
      pipelinegenomemethylation
      pipelinegenomemethylationdna-methylationwgbsbismark
      Python
      •
      GNU General Public License v3.0
      •7•39•5•0•Updated Jul 12, 2026Jul 12, 2026

    • simSOMA-tutorial

      Public
      simSOMA-tutorial
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jun 26, 2026Jun 26, 2026

    • simSOMA

      Public
      simSOMA is a cell-lineage based simulator of somatic variant allele-frequency (VAF) spectra in plants
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 26, 2026Jun 26, 2026

    • polymer-penalty

      Public
      Code for applying a polymer physics-based penalty to correct distance bias in chromatin interaction data.
      Jupyter Notebook
      •0•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • jDMRgrid

      Public
      jDMRgrid: a heuristic DMR caller for WGBS data using grid approach
      R
      •1•0•0•1•Updated Sep 20, 2025Sep 20, 2025

    • Mapping-genetic-modifiers-of-epimutation-rates_Zhang-et-al

      Public
      ATAC-seq Analysis Pipeline for Arabidopsis thaliana
      Shell
      •1•1•0•0•Updated Jun 12, 2025Jun 12, 2025

    • samSFS

      Public
      R
      •
      Other
      •0•0•0•0•Updated May 27, 2025May 27, 2025

    • GenomicLinks

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 8, 2024May 8, 2024

    • gbMine

      Public
      Automatic detection of gene body methylated genes in plant genomes
      Python
      •0•0•0•0•Updated Feb 8, 2024Feb 8, 2024

    • AlphaBeta

      Public
      Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
      geneticscomputational-biologyepigenetics
      geneticscomputational-biologyepigenetics
      R
      •
      GNU General Public License v3.0
      •2•10•1•1•Updated Jan 4, 2023Jan 4, 2023

    • Zhang-et-al-project

      Public
      R
      •1•0•0•0•Updated May 14, 2021May 14, 2021

    • mutSOMA

      Public
      R
      •0•1•0•0•Updated Jul 11, 2019Jul 11, 2019

    • Number-Sepration

      Public
      GNU General Public License v2.0
      •0•0•0•0•Updated Jan 15, 2014Jan 15, 2014
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