Repositories list

• CancerMutationDetectionCourse

  Public
  Google colab notebook for cancer mutation detection taster lecture

  Jupyter Notebook

  •0•0•0•0•Updated Mar 13, 2026Mar 13, 2026

• gghic

  Public
  gghic makes visualization of Hi-C/-like data easily in R

  ggplot2rhic+ 4

  ggplot2rhic3d-genomegenomics-visualizationgenomic-interactionspore-c

  R

  •

  GNU General Public License v3.0

  •1•25•1•0•Updated Jan 23, 2026Jan 23, 2026

• cfDNA_deconv

  Public
  For deconvolution of cfDNA or other DNA mixture composition by leveraging read-level methylation signals

  Python

  •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

• NPC_GeneSignature

  Public
  A cross-platform gene signature to predict survival outcomes for nasopharyngeal carcinoma

  Jupyter Notebook

  •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

• smk_sv

  Public
  A snakemake pipeline to call structure variants from ONT data

  bioinformaticsbioinformatics-pipelinestructural-variations+ 4

  bioinformaticsbioinformatics-pipelinestructural-variationsstructural-variantslong-read-sequencingstructural-variation-callingoxford-nanopore-sequencing

  Python

  •0•2•0•0•Updated Nov 7, 2025Nov 7, 2025

• HKU-Practical-Bioinformatics

  Public
  HTML

  •0•1•0•0•Updated Oct 27, 2025Oct 27, 2025

• git-and-github-rachelkhl

  Public
  biof3002-2025-git-and-github-github-starter-course created by GitHub Classroom

  1•0•0•0•Updated Sep 26, 2025Sep 26, 2025

• biof3002-2025-git-and-github-github-starter-course

  Public
  biof3002-2025-git-and-github-github-starter-course created by GitHub Classroom

  1•0•0•0•Updated Sep 26, 2025Sep 26, 2025

• BIOF3001

  Public
  Epigenetic clock

  MIT License

  •0•0•0•0•Updated Sep 22, 2025Sep 22, 2025

• LocusMasterTE

  Public
  Integrating long read sequencing enhances short read-based locus-specific transposable element quantification

  Python

  •

  MIT License

  •0•10•3•0•Updated May 12, 2025May 12, 2025

• biof2014

  Public
  Week 13 tutorial

  0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

• LocusMasterTE_paper

  Public
  Scripts for figures and results in LocusMasterTE paper

  R

  •

  MIT License

  •0•0•0•0•Updated Feb 1, 2025Feb 1, 2025

• SpecAlign

  Public
  Windows version for processing and alignment of mass spectra datasets.

  C++

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

• ERVK-7

  Public
  R

  •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• ERCC2

  Public
  Scripts for Barbour et al. ERCC2 mutations alter the genomic distribution pattern of somatic mutations and are independently prognostic in bladder cancer

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 7, 2024Jul 7, 2024

• withings_api_dev

  Public
  Template for flask application to access Withings API

  Python

  •0•0•0•1•Updated May 21, 2024May 21, 2024

• GenomicsWorkshop

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 28, 2024Feb 28, 2024

• HKU_STEM

  Public
  HKU STEM Data Science Lab for SARS-CoV2 bioinformatics

  Jupyter Notebook

  •0•0•0•0•Updated Jul 22, 2023Jul 22, 2023

• genomics-exercise

  Public
  Genomics exercise from Jason Wong lab @ HKU

  MIT License

  •2•0•0•0•Updated Oct 14, 2022Oct 14, 2022

• TMB

  Public
  Tumour mutation burden correction

  MIT License

  •1•2•0•1•Updated Oct 14, 2022Oct 14, 2022

• cBioportalDataClawler

  Public
  Some simple Python scripts to download data files from https://www.cbioportal.org/

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 4, 2022Jan 4, 2022

• RNAseq-analysis-pipeline

  Public
  This guidebook aims to demonstrate the RNA-seq analysis pipeline and the basics statistical analysis behind Differential Gene expression detection

  Jupyter Notebook

  •2•2•0•0•Updated Jun 9, 2021Jun 9, 2021

• MMR

  Public
  R

  •1•0•0•0•Updated Oct 9, 2020Oct 9, 2020