Repositories list

• MCube

  Public
  A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies

  spatial-transcriptomicsspatially-variable-genesstatistical-hypothesis-testing

  R

  •

  GNU General Public License v3.0

  •0•6•0•0•UpdatedMay 13, 2025May 13, 2025

• UGPhysics

  Public
  Official Repository of UGPhysics Benchmark [ICML 2025]

  Python

  •1•10•0•0•UpdatedMay 1, 2025May 1, 2025

• FLAG

  Public
  Flexible and Accurate Methods for Estimation and Inference of Gaussian Graphical Models with Applications

  rgaussian-graphical-modelsprecision-matrix+ 5empirical-bayesrandom-effects-modelstatistical-inference-for-data-sciencejoint-estimationlow-rank-update

  Jupyter Notebook

  •

  Other

  •0•5•0•0•UpdatedApr 23, 2025Apr 23, 2025

• mfair

  Public
  mfair: Matrix Factorization with Auxiliary Information in R

  rmatrix-factorizationexpectation-maximization-algorithm+ 5variational-inferencematrix-completiongradient-boostinglow-rankempirical-bayes

  R

  •

  Other

  •1•8•0•0•UpdatedApr 21, 2025Apr 21, 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

  •0•4•0•0•UpdatedApr 18, 2025Apr 18, 2025

• MR-APSS

  Public
  Mendelian Randomization accounting for Pleiotropy and Sample Structure using genome-wide summary statistics

  R

  •10•42•4•1•UpdatedApr 8, 2025Apr 8, 2025

• STIMP

  Public
  Jupyter Notebook

  •0•2•0•0•UpdatedMar 6, 2025Mar 6, 2025

• XMAP

  Public
  HTML

  •0•9•1•0•UpdatedDec 19, 2024Dec 19, 2024

• MATH-4432-Statistical-Machine-Learning

  Public
  Tutorials for MATH 4432 Statistical Machine Learning, 2024 Fall

  HTML

  •1•14•0•0•UpdatedDec 12, 2024Dec 12, 2024

• MRbenchmarking

  Public
  R

  •0•8•0•0•UpdatedOct 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•UpdatedSep 15, 2024Sep 15, 2024

• UCS

  Public
  Code for "UCS: a unified approach to cell segmentation for subcellular spatial transcriptomics"

  Jupyter Notebook

  •1•6•3•0•UpdatedJul 30, 2024Jul 30, 2024

• XPASS

  Public
  Cross-population analysis using GWAS summary statistics

  R

  •6•18•4•1•UpdatedJun 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

  •7•63•12•0•UpdatedMay 24, 2024May 24, 2024

• STitch3D

  Public
  Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices

  deep-learning3d-reconstructionspatial-transcriptomics

  Python

  •

  MIT License

  •4•63•16•0•UpdatedNov 20, 2023Nov 20, 2023

• PALM

  Public
  Python

  •

  MIT License

  •0•6•0•0•UpdatedNov 15, 2023Nov 15, 2023

• 3DVesselSegNet

  Public
  hybrid representation learning approach for fully automatic and template-free vessel centerline extraction

  Jupyter Notebook

  •0•10•0•0•UpdatedJul 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•UpdatedJul 13, 2023Jul 13, 2023

• SpatialScope-Beta

  Public
  Python

  •0•0•0•0•UpdatedFeb 7, 2023Feb 7, 2023

• LOG-TRAM

  Public
  Python

  •

  MIT License

  •1•9•1•0•UpdatedJul 8, 2022Jul 8, 2022

• XPXP

  Public
  Jupyter Notebook

  •0•0•0•0•UpdatedMay 24, 2022May 24, 2022

• MRAPSS_RealDataAnalysis_reproduce

  Public
  R code for reproduce real data analysis in MRAPSS paper.

  mrinsidepleiotropy+ 3mendelian-randomizationselection-biascorrelated-pleiotropy

  HTML

  •0•2•0•0•UpdatedMay 6, 2022May 6, 2022

• DGLSB

  Public
  Deep Generative Learning via Schrödinger Bridge

  Python

  •3•23•0•0•UpdatedNov 1, 2021Nov 1, 2021

• GPU-LMM

  Public
  C++

  •0•0•0•0•UpdatedMar 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•1•0•0•UpdatedNov 1, 2020Nov 1, 2020

• VGrow-Pg

  Public
  A tensorflow implementation of VGrow by using progressive growing method.

  Python

  •0•2•0•0•UpdatedOct 21, 2020Oct 21, 2020

• XPA

  Public
  Cross-population analysis using the individual-level GWAS data

  C++

  •

  GNU General Public License v3.0

  •0•1•1•0•UpdatedSep 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•UpdatedJul 15, 2020Jul 15, 2020

• iGREX

  Public
  Quantifying the impact of genetically regulated expression on complex traits and diseases

  C++

  •1•0•0•0•UpdatedJun 26, 2020Jun 26, 2020

• BWMR

  Public
  BWMR (Bayesian Weighted Mendelian Randomization)

  R

  •0•0•0•0•UpdatedJun 22, 2020Jun 22, 2020