Repositories list

• UGPhysics

  Public
  Official Repository of UGPhysics Benchmark

  Python

  •0•1•0•0•Updated Feb 5, 2025Feb 5, 2025

• MCube

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

  statistical-modelingspatial-transcriptomicsspatially-variable-genes+ 1statistical-hypothesis-testing

  R

  •

  GNU General Public License v3.0

  •0•4•0•0•Updated Feb 4, 2025Feb 4, 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•Updated Jan 25, 2025Jan 25, 2025

• STIMP

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Jan 23, 2025Jan 23, 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

• 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•9•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.

  mrinsidepleiotropy+ 3mendelian-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•1•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•1•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•0•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