Skip to content

@YangLabHKUST YangLab@HKUST

Change the repository type filter

All

    Repositories list

    52 repositories

    • stGP

      Public
      stGP: Characterizing dynamic tissue architectures by identifying cell-type-specific spatiotemporal gene programs
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jul 16, 2026Jul 16, 2026

    • ST-CNABench

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 8, 2026Jul 8, 2026

    • STD-Hunter

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 5, 2026Jul 5, 2026

    • MCube

      Public
      A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies
      spatial-transcriptomicsspatially-variable-genespenalized-quasi-likelihood
      spatial-transcriptomicsspatially-variable-genespenalized-quasi-likelihoodvariance-component-testing
      R
      •
      GNU General Public License v3.0
      •0•8•0•0•Updated Jul 4, 2026Jul 4, 2026

    • flow-matching-for-single-cell-dynamic-biology

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 26, 2026Jun 26, 2026

    • Variational_Inference_Tutorial

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • STAT-agent

      Public
      STAT: Spatial Transcriptomics Analytical agenT - AI-powered platform for spatial omics analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated May 12, 2026May 12, 2026

    • MR-APSS

      Public
      Mendelian Randomization accounting for Pleiotropy and Sample Structure using genome-wide summary statistics
      R
      •
      MIT License
      •10•44•5•1•Updated Apr 30, 2026Apr 30, 2026

    • Harmonics

      Public
      Hierarchical distribution matching enables comprehensive characterization of common and condition-specific cell niches in spatial omics data
      Python
      •
      MIT License
      •0•6•0•0•Updated Mar 28, 2026Mar 28, 2026

    • CellART

      Public
      Python
      •
      MIT License
      •0•12•0•0•Updated Mar 26, 2026Mar 26, 2026

    • XMR

      Public
      XMR: A cross-population Mendelian randomization method for causal inference using genome-wide summary statistics
      HTML
      •
      GNU General Public License v3.0
      •0•4•1•0•Updated Mar 20, 2026Mar 20, 2026

    • XMR_reproduce

      Public
      Reproduction of results in XMR paper
      Jupyter Notebook
      •0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

    • SyncTrack

      Public
      Python
      •0•4•0•0•Updated Mar 8, 2026Mar 8, 2026

    • UGPhysics

      Public
      Official Repository of UGPhysics Benchmark [ICML 2025]
      Python
      •17•122•2•0•Updated Feb 24, 2026Feb 24, 2026

    • MATH-4432-Statistical-Machine-Learning

      Public
      Tutorials for MATH 4432 Statistical Machine Learning, 2025 Fall
      HTML
      •4•20•0•0•Updated Nov 26, 2025Nov 26, 2025

    • MacSGP

      Public
      MacSGP: Mapping Cell-Type-Specific Spatial Gene Programs Uncovers Tissue Architecture and Microenvironment Organization
      deep-learningspatial-transcriptomicsgene-program
      deep-learningspatial-transcriptomicsgene-program
      Python
      •
      MIT License
      •0•3•0•0•Updated Nov 24, 2025Nov 24, 2025

    • NBAvatar

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Jun 30, 2025Jun 30, 2025

    • FLAG

      Public
      Flexible and Accurate Methods for Estimation and Inference of Gaussian Graphical Models with Applications
      rgaussian-graphical-modelsprecision-matrix
      rgaussian-graphical-modelsprecision-matrixempirical-bayesrandom-effects-modelstatistical-inference-for-data-sciencejoint-estimationlow-rank-update
      Jupyter Notebook
      •
      Other
      •0•5•0•0•Updated Jun 22, 2025Jun 22, 2025

    • UCS

      Public
      Code for "UCS: a unified approach to cell segmentation for subcellular spatial transcriptomics"
      Jupyter Notebook
      •
      MIT License
      •3•10•3•0•Updated May 22, 2025May 22, 2025

    • UGMathBench

      Public
      Official Repo of UGMathBench: A Diverse and Dynamic Benchmark for Undergraduate-Level Mathematical Reasoning with Large Language Models [ICLR 2025]
      Python
      •
      GNU General Public License v3.0
      •2•9•0•0•Updated May 20, 2025May 20, 2025

    • STIMP

      Public
      Jupyter Notebook
      •2•20•1•0•Updated May 19, 2025May 19, 2025

    • mfair

      Public
      mfair: Matrix Factorization with Auxiliary Information in R
      rmatrix-factorizationexpectation-maximization-algorithm
      rmatrix-factorizationexpectation-maximization-algorithmvariational-inferencematrix-completiongradient-boostinglow-rankempirical-bayes
      R
      •
      Other
      •0•9•0•0•Updated Apr 21, 2025Apr 21, 2025

    • XMAP

      Public
      HTML
      •1•10•2•0•Updated Dec 19, 2024Dec 19, 2024

    • MRbenchmarking

      Public
      R
      •0•9•0•0•Updated Oct 16, 2024Oct 16, 2024

    • SRT_alignment_and_integration

      Public
      Measurement and comparison of several slices aligning methods and data integrating mathods for spatial transcriptomics data using several ST datasets.
      Python
      •0•7•0•0•Updated Sep 15, 2024Sep 15, 2024

    • XPASS

      Public
      Cross-population analysis using GWAS summary statistics
      R
      •5•20•4•1•Updated Jun 25, 2024Jun 25, 2024

    • SpatialScope

      Public
      A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models
      Python
      •
      GNU General Public License v3.0
      •9•82•14•0•Updated May 24, 2024May 24, 2024

    • STitch3D

      Public
      Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
      deep-learning3d-reconstructionspatial-transcriptomics
      deep-learning3d-reconstructionspatial-transcriptomics
      Python
      •
      MIT License
      •6•72•17•0•Updated Nov 20, 2023Nov 20, 2023

    • PALM

      Public
      Python
      •
      MIT License
      •0•6•0•0•Updated Nov 15, 2023Nov 15, 2023

    • 3DVesselSegNet

      Public
      hybrid representation learning approach for fully automatic and template-free vessel centerline extraction
      Jupyter Notebook
      •0•12•0•0•Updated Jul 17, 2023Jul 17, 2023
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.