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    36 repositories

    • MCube

      Public
      A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies
      spatial-transcriptomicsspatially-variable-genes
      R
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Jan 24, 2025Jan 24, 2025

    • MR-APSS

      Public
      Mendelian Randomization accounting for Pleiotropy and Sample Structure using genome-wide summary statistics
      R
      •10•41•3•1•Updated Jan 9, 2025Jan 9, 2025

    • XMAP

      Public
      HTML
      •0•9•1•0•Updated Dec 19, 2024Dec 19, 2024

    • MATH-4432-Statistical-Machine-Learning

      Public
      Tutorials for MATH 4432 Statistical Machine Learning, 2024 Fall
      HTML
      •1•14•0•0•Updated Dec 12, 2024Dec 12, 2024

    • MRbenchmarking

      Public
      R
      •0•7•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•5•0•0•Updated Sep 15, 2024Sep 15, 2024

    • UCS

      Public
      Code for "UCS: a unified approach to cell segmentation for subcellular spatial transcriptomics"
      Jupyter Notebook
      •0•3•1•0•Updated Jul 30, 2024Jul 30, 2024

    • XPASS

      Public
      Cross-population analysis using GWAS summary statistics
      R
      •6•18•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
      •6•58•11•0•Updated May 24, 2024May 24, 2024

    • mfair

      Public
      mfair: Matrix Factorization with Auxiliary Information in R
      rmatrix-factorizationexpectation-maximization-algorithmvariational-inferencematrix-completiongradient-boostinglow-rankempirical-bayes
      R
      •
      Other
      •1•8•0•0•Updated Feb 1, 2024Feb 1, 2024

    • STitch3D

      Public
      Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
      deep-learning3d-reconstructionspatial-transcriptomics
      Python
      •
      MIT License
      •3•59•16•0•Updated Nov 20, 2023Nov 20, 2023

    • PALM

      Public
      Python
      •
      MIT License
      •0•5•0•0•Updated Nov 15, 2023Nov 15, 2023

    • FLAG

      Public
      Flexible and Accurate Methods for Estimation and Inference of Gaussian Graphical Models with Applications
      Jupyter Notebook
      •0•5•0•0•Updated Oct 15, 2023Oct 15, 2023

    • 3DVesselSegNet

      Public
      hybrid representation learning approach for fully automatic and template-free vessel centerline extraction
      Jupyter Notebook
      •0•8•0•0•Updated Jul 17, 2023Jul 17, 2023

    • Portal

      Public
      Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets
      deep-learningdata-integrationsingle-cell-analysis
      Python
      •
      MIT License
      •6•30•4•0•Updated Jul 13, 2023Jul 13, 2023

    • SpatialScope-Beta

      Public
      Python
      •0•0•0•0•Updated Feb 7, 2023Feb 7, 2023

    • LOG-TRAM

      Public
      Python
      •
      MIT License
      •1•10•1•0•Updated Jul 8, 2022Jul 8, 2022

    • XPXP

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 24, 2022May 24, 2022

    • MRAPSS_RealDataAnalysis_reproduce

      Public
      R code for reproduce real data analysis in MRAPSS paper.
      mrinsidepleiotropymendelian-randomizationselection-biascorrelated-pleiotropy
      HTML
      •0•2•0•0•Updated May 6, 2022May 6, 2022

    • DGLSB

      Public
      Deep Generative Learning via Schrödinger Bridge
      Python
      •3•20•0•0•Updated Nov 1, 2021Nov 1, 2021

    • GPU-LMM

      Public
      C++
      •0•0•0•0•Updated Mar 3, 2021Mar 3, 2021

    • VCM

      Public
      R package VCM contains three approaches for solving variance components model: PX-EM algorithm, MM algorithm and Method of Moments
      R
      •4•2•0•0•Updated Nov 1, 2020Nov 1, 2020

    • VGrow-Pg

      Public
      A tensorflow implementation of VGrow by using progressive growing method.
      Python
      •0•2•0•0•Updated Oct 21, 2020Oct 21, 2020

    • XPA

      Public
      Cross-population analysis using the individual-level GWAS data
      C++
      •
      GNU General Public License v3.0
      •0•2•1•0•Updated Sep 18, 2020Sep 18, 2020

    • scPI

      Public
      scPI: A scalable framework for probabilistic inference insingle-cell RNA-sequencing data analysis
      Jupyter Notebook
      •1•1•0•0•Updated Jul 15, 2020Jul 15, 2020

    • iGREX

      Public
      Quantifying the impact of genetically regulated expression on complex traits and diseases
      C++
      •1•1•0•0•Updated Jun 26, 2020Jun 26, 2020

    • BWMR

      Public
      BWMR (Bayesian Weighted Mendelian Randomization)
      R
      •0•0•0•0•Updated Jun 22, 2020Jun 22, 2020

    • FIRM

      Public
      Fast Integration of single-cell RNA-sequencing data across Multiple platforms
      C++
      •0•0•0•0•Updated Jun 5, 2020Jun 5, 2020

    • LPM-sim

      Public
      Simulation codes to reproduce the results in the LPM paper
      R
      •0•0•0•0•Updated Jun 5, 2020Jun 5, 2020

    • LSMM-sim

      Public
      Simulation codes and example to reproduce the results in the LSMM paper
      R
      •0•0•0•0•Updated Jun 5, 2020Jun 5, 2020