Repositories list

• SMOPINseqTools

  Public
  Python

  •0•0•0•0•Updated Jan 19, 2026Jan 19, 2026

• iPRINT-Tools

  Public
  Data decoding pipeline to process iPRINT-seq fastq data

  Python

  •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

• 4DN-Web-Portal

  Public
  Web Portal for 4DN

  HTML

  •0•0•0•0•Updated Apr 25, 2025Apr 25, 2025

• breast_cancer_recurrence_classifier

  Public
  2•1•0•0•Updated Mar 30, 2025Mar 30, 2025

• project_sample_code

  Public
  Course project: Breast cancer classifier based on silver-seq data

  R

  •0•0•0•0•Updated Mar 30, 2025Mar 30, 2025

• PRIMseqTools

  Public
  Python

  •0•6•1•0•Updated Jan 27, 2025Jan 27, 2025

• PROPERseqTools

  Public
  Python

  •1•5•1•0•Updated Jan 11, 2025Jan 11, 2025

• BENG183_2024Fall_Applied-Genomic-Technologies

  Public
  Repo for BENG 183 Applied Genomic Technologies 2024 Fall

  Jupyter Notebook

  •52•3•0•0•Updated Dec 15, 2024Dec 15, 2024

• MUSIC-tools

  Public
  R

  •0•5•0•0•Updated Oct 20, 2024Oct 20, 2024

• AD_prediction_blood

  Public
  1•0•0•0•Updated May 1, 2024May 1, 2024

• MUSIC-docker

  Public
  Python

  •1•2•0•0•Updated Mar 15, 2024Mar 15, 2024

• MUSIC-Snakemake

  Public
  Python

  •0•1•0•0•Updated Mar 3, 2024Mar 3, 2024

• HiFislides

  Public
  Processing pipeline for the HiFi-Slides technology developed in the Sheng Zhong Lab.

  R

  •0•0•0•0•Updated Feb 6, 2024Feb 6, 2024

• RNA3Dgenome-code-repository

  Public
  Collection of all the codes used for the paper "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells…

  R

  •1•7•0•0•Updated Dec 17, 2023Dec 17, 2023

• BENG183_2023Fall_Applied-Genomic-Technologies

  Public
  Repository for BENG 183 Applied Genomic Technologies

  44•1•0•0•Updated Dec 15, 2023Dec 15, 2023

• BENG183

  Public
  Lecture materials

  82•3•0•4•Updated Dec 14, 2023Dec 14, 2023

• IVF_data_analysis

  Public
  Python

  •0•0•0•0•Updated Nov 15, 2023Nov 15, 2023

• EpiAlignment_WebApp

  Public
  EpiAlignment web service

  HTML

  •

  Apache License 2.0

  •0•0•1•7•Updated Mar 4, 2023Mar 4, 2023

• Genomic-Interactive-Visualization-Engine

  Public
  Genomic Interactive Visualization Engine

  javascriptgenomics-visualizationepigenetic-data+ 1

  javascriptgenomics-visualizationepigenetic-datagenomic-interactions

  JavaScript

  •

  Apache License 2.0

  •32•145•17•12•Updated Jan 5, 2023Jan 5, 2023

• chrom-region

  Public
  Chromosomal region class used in GIVE, supporting some basic region operations

  JavaScript

  •

  Apache License 2.0

  •0•0•0•13•Updated Jan 3, 2023Jan 3, 2023

• BENG183_2022Fall_Applied-Genomic-Technologies

  Public
  Repository for 2022Fall BENG 183 Applied Genomic Technologies

  Jupyter Notebook

  •45•4•0•0•Updated Dec 12, 2022Dec 12, 2022

• GenomePlot

  Public
  Plot bedfiles over the entire genome with chromIdeoBands

  JavaScript

  •

  Apache License 2.0

  •1•0•0•9•Updated Dec 8, 2022Dec 8, 2022

• Genomic-Interactive-Visualization-Engine-1

  Public
  Genomic Interactive Visualization Engine

  JavaScript

  •

  Apache License 2.0

  •32•0•0•0•Updated May 25, 2022May 25, 2022

• iMARGI-Docker

  Public
  iMARGI-Docker distributes the iMARGI sequencing data processing pipeline

  dockerpipelinesequencing+ 3

  dockerpipelinesequencinginteractionrna-dnaimargi

  Shell

  •5•3•1•0•Updated Jan 19, 2022Jan 19, 2022

• NCOMMS-19-24818

  Public
  Repository of codes used in the paper NCOMMS-19-24818

  R

  •0•1•0•0•Updated Jun 11, 2021Jun 11, 2021

• BENG183_FA2020_courseproject

  Public
  HTML

  •37•0•0•0•Updated Dec 18, 2020Dec 18, 2020

• Applied-Genomic-Technologies

  Public
  4•0•0•1•Updated Dec 15, 2020Dec 15, 2020

• HiCtool

  Public
  Python library for processing and visualizing Hi-C data

  Python

  •7•20•1•0•Updated May 31, 2020May 31, 2020

• breastCancerClassifier

  Public
  R

  •0•0•0•0•Updated Apr 3, 2020Apr 3, 2020

• MapSilverSeqDataWithExceRpt

  Public
  Python

  •0•0•0•0•Updated Mar 2, 2020Mar 2, 2020