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    21 repositories

    • iscream

      Public
      Make fast and memory efficient BED file queries, summaries, and matrices.
      rcppbedwgbstabix
      R
      •
      Other
      •1•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • tranquillyzer

      Public
      Python
      •2•1•0•0•Updated Aug 22, 2025Aug 22, 2025

    • compartmap

      Public
      Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq
      scrna-seqscatac-seq
      R
      •
      Other
      •10•14•12•10•Updated Aug 6, 2025Aug 6, 2025

    • tranquillyzer_manuscript_code

      Public
      Code used in the manuscript for Tranquillyzer
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • iscream.paper

      Public
      R
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • Biscuit_Snakemake_Workflow

      Public
      Snakemake Workflow For Running Biscuit https://github.com/huishenlab/biscuit
      methylationwgbs
      Python
      •
      GNU General Public License v3.0
      •12•3•1•0•Updated May 22, 2025May 22, 2025

    • biscuit

      Public
      BISulfite-seq CUI Toolkit
      C
      •
      Other
      •24•24•8•1•Updated May 13, 2025May 13, 2025

    • STORMqc

      Public
      QC pipeline for STORM data
      Python
      •
      MIT License
      •1•1•0•0•Updated Apr 25, 2025Apr 25, 2025

    • Fallopian_tube_multiomics

      Public
      Analysis code for <link to be inserted when published>
      MIT License
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • dupsifter

      Public
      WGBS/WGS PCR Duplicate Marking
      C
      •
      MIT License
      •2•6•1•0•Updated Nov 13, 2024Nov 13, 2024

    • bsseq

      Public
      Devel repository for bsseq
      R
      •28•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • TE_quantification_snakemake

      Public
      R
      •2•2•0•0•Updated Jan 30, 2024Jan 30, 2024

    • sgsl

      Public
      A lightweight subset of GNU scientific library
      C
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 25, 2023Oct 25, 2023

    • utils

      Public
      some utility C code
      C
      •
      Apache License 2.0
      •1•0•0•0•Updated Oct 25, 2023Oct 25, 2023

    • bisplotti

      Public
      Plotting package for bisulfite sequencing and methylation arrays
      R
      •
      GNU General Public License v3.0
      •6•7•0•0•Updated Sep 18, 2023Sep 18, 2023

    • biscuit_paper_code

      Public
      Scripts and Templates For Results in the BISCUIT Paper
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 12, 2023Sep 12, 2023

    • sv_calling_docker

      Public
      This repository contains a dockerfile and build script to make a container for SV calling from WG(B)S
      Dockerfile
      •
      MIT License
      •0•2•0•0•Updated Jul 18, 2023Jul 18, 2023

    • TE_quantification_pipeline

      Public
      R
      •2•2•1•0•Updated May 12, 2023May 12, 2023

    • STORM_seq_automation

      Public
      This repository contains the automation scripts for STORM-seq
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 28, 2022Jul 28, 2022

    • multiscale_methylation_plot_pipeline

      Public
      Snakemake pipeline to generate multiscale methylation plots
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 17, 2022Feb 17, 2022

    • biscuitBlaster

      Public
      Alignment pipeline for biscuit
      Shell
      •
      MIT License
      •1•0•0•0•Updated Nov 18, 2020Nov 18, 2020