Repositories list

• HLab-pubmon

  Public
  Publication monitoring at Huang Lab

  TeX

  •99 forks•77 stars•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• inDecay

  Public
  Cell type-aware CRISPR editing outcomes prediction

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• FineST

  Public
  Fine-grained Spatial Transcriptomics by integrating paired histology image

  weak-supervisionspatial-transcriptomicscontrastive-learning+ 3

  weak-supervisionspatial-transcriptomicscontrastive-learningcell-cell-communicationhistology-imagesligand-receptor-interaction

  Jupyter Notebook

  •

  Apache License 2.0

  •22 forks•1919 stars•00 issues•00 pull requests•Updated Mar 30, 2026Mar 30, 2026

• CRAK-Velo

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •22 forks•44 stars•00 issues•00 pull requests•Updated Mar 27, 2026Mar 27, 2026

• bioinfo-book

  Public
  Book placeholder for Sequence Bioinformatics

  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 20, 2026Mar 20, 2026

• statbiomed.github.io

  Public
  GitHub page of statistical learning for biomedicine

  CSS

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 22, 2026Feb 22, 2026

• HKUbioinfoNet

  Public
  HKU Bioinformatics Seminars

  00 forks•44 stars•00 issues•00 pull requests•Updated Jan 6, 2026Jan 6, 2026

• TemporalVAE-reproducibility

  Public
  Python

  •00 forks•44 stars•00 issues•00 pull requests•Updated Dec 18, 2025Dec 18, 2025

• xDecoder

  Public
  xDecoder unlocks the potential of foundation models for few-shot personal gene expression prediction

  Python

  •

  MIT License

  •11 fork•55 stars•00 issues•00 pull requests•Updated Nov 27, 2025Nov 27, 2025

• sbms-server

  Public
  School of Biomedical Sciences (HKU) server wiki repository

  66 forks•55 stars•00 issues•33 pull requests•Updated Nov 24, 2025Nov 24, 2025

• BMDS-book

  Public
  Biomedical Data Science book

  case-studiesr-programmingbiomedical-data-science

  case-studiesr-programmingbiomedical-data-science

  HTML

  •

  Creative Commons Zero v1.0 Universal

  •44 forks•99 stars•00 issues•11 pull request•Updated Nov 21, 2025Nov 21, 2025

• SNPmanifold

  Public
  Manifold learning for single-cell single-nucleotide genetic variations

  single-cellmanifold-learninggenetic-variants+ 1

  single-cellmanifold-learninggenetic-variantsvariational-autoencoder

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks•44 stars•00 issues•00 pull requests•Updated Oct 23, 2025Oct 23, 2025

• promoter_activity

  Public
  This repository includes codes plotting figures in "Alternative promoter during mammalian organ development"

  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 21, 2025Sep 21, 2025

• TemporalVAE

  Public
  TemporalVAE: dual-objective VAE for time prediction in single cells

  variational-autoencodersingle-cell-rna-seqtime-prediction+ 2

  variational-autoencodersingle-cell-rna-seqtime-predictiontime-series-scrnaseqsingle-cell-atlas

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•1313 stars•22 issues•00 pull requests•Updated Sep 13, 2025Sep 13, 2025

• SpatialDM

  Public
  Spatial direct messaging detected by bivariate Moran

  spatial-transcriptomicsspatial-correlationcell-cell-communication+ 1

  spatial-transcriptomicsspatial-correlationcell-cell-communicationligand-receptor-interaction

  Jupyter Notebook

  •

  Apache License 2.0

  •66 forks•3131 stars•1616 issues•11 pull request•Updated Jul 16, 2025Jul 16, 2025

• clonaltrans

  Public
  Estimation of clone-specific dynamical transition rate

  Jupyter Notebook

  •

  MIT License

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jul 5, 2025Jul 5, 2025

• Embryo2live

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 1, 2025Jul 1, 2025

• scTail

  Public
  Detection and quantify alternative polyA site

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks•44 stars•33 issues•00 pull requests•Updated Jun 28, 2025Jun 28, 2025

• LogisticGLM

  Public
  Implementation of logistic regression and basic neural network

  00 forks•00 stars•00 issues•00 pull requests•Updated Jun 24, 2025Jun 24, 2025

• DNA-AI-hackathon

  Public
  DNA AI Hackathon

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 2, 2025Apr 2, 2025

• stemVAE_endometrium

  Public
  Version: alph; Time: 231128; Owner: awa121

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jan 19, 2025Jan 19, 2025

• UniTVelo

  Public
  UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference

  velocityinferencerna+ 2

  velocityinferencernatranscriptomicstrajectory

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1010 forks•2727 stars•44 issues•00 pull requests•Updated Nov 12, 2024Nov 12, 2024

• HKSingleCell2022

  Public
  Workshop on single cell data science 2022

  conference-websitesingle-cell-data-science

  conference-websitesingle-cell-data-science

  00 forks•00 stars•00 issues•00 pull requests•Updated May 29, 2024May 29, 2024

• CamoTSS

  Public
  Detection and couting alternative TSS in single cells

  Jupyter Notebook

  •

  Apache License 2.0

  •55 forks•1717 stars•88 issues•00 pull requests•Updated Apr 21, 2024Apr 21, 2024

• BBMix

  Public
  Inference of Beta-binomial mixture model

  Python

  •

  Apache License 2.0

  •11 fork•33 stars•11 issue•00 pull requests•Updated Oct 11, 2023Oct 11, 2023

• NegabinGLM

  Public
  NegabinGLM: Negative-binomial regression model

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 18, 2023Jul 18, 2023

• SpatialCV

  Public
  Spatial Co-Variable gene pair analysis

  Python

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 8, 2022Nov 8, 2022

• BetabinGLM

  Public
  Beta-binomial regression model

  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 2, 2022Nov 2, 2022

• GLM-hackathon

  Public
  Hackathon on GLM implementation for summer internship

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 30, 2022Jul 30, 2022

• HKU-single-cell-workshop

  Public
  Single-cell analysis workshop at HKU

  22 forks•77 stars•00 issues•00 pull requests•Updated Jul 25, 2022Jul 25, 2022