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    36 repositories

    • DeepLearningTheory.course.2024

      Public
      Deep Learning Theory course
      4•2•0•0•Updated Dec 19, 2024Dec 19, 2024

    • STALocator

      Public
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Dec 14, 2024Dec 14, 2024

    • TADGATE

      Public
      TADGATE is a computational tool to identify TADs in Hi-C contact map with a graph attention autoencoder.
      Jupyter Notebook
      •
      MIT License
      •1•2•0•1•Updated Dec 10, 2024Dec 10, 2024

    • Mactop

      Public
      deciphering chromatin domain, domain community and chromunity for 3D genome maps
      Jupyter Notebook
      •
      MIT License
      •3•1•0•0•Updated Oct 18, 2024Oct 18, 2024

    • STADIA

      Public
      C++
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Oct 15, 2024Oct 15, 2024

    • STAMapper

      Public
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Oct 8, 2024Oct 8, 2024

    • BrainAlign

      Public
      Code for "Whole brain alignment of spatial transcriptomics between humans and mice with BrainAlign"
      brainspatial-transcriptomicscross-species
      Python
      •
      MIT License
      •2•10•0•0•Updated Oct 4, 2024Oct 4, 2024

    • STABox

      Public
      Interactive analysis and visualization of spatial transcriptome GUI program
      Jupyter Notebook
      •4•0•0•1•Updated Jul 29, 2024Jul 29, 2024

    • STAMarker

      Public
      STAMarker: Identify Spatial Domain-specific Variable Genes via Ensemble Graph Attention Autoencoders
      Jupyter Notebook
      •4•4•0•0•Updated Jul 16, 2024Jul 16, 2024

    • STASCAN

      Public
      Python
      •
      MIT License
      •5•0•0•0•Updated Jul 15, 2024Jul 15, 2024

    • ImputeHiFI

      Public
      ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single-Cell Hi-C and RNA FISH Data
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Jun 8, 2024Jun 8, 2024

    • STAGE

      Public
      Jupyter Notebook
      •
      MIT License
      •2•8•0•0•Updated Jun 5, 2024Jun 5, 2024

    • CAMEX

      Public
      Jupyter Notebook
      •
      MIT License
      •3•1•0•0•Updated Apr 13, 2024Apr 13, 2024

    • STAligner

      Public
      STAligner: Integrating spatial transcriptomics data across different conditions, technologies, and developmental stages
      Jupyter Notebook
      •
      MIT License
      •5•19•0•0•Updated Dec 26, 2023Dec 26, 2023

    • CAME

      Public
      Cell-type Assignment and Module Extraction based on a heterogeneous graph neural network.
      Python
      •
      MIT License
      •6•8•0•1•Updated Oct 30, 2023Oct 30, 2023

    • ConsTADs

      Public
      Consensus TADs
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Jul 11, 2023Jul 11, 2023

    • AI4OR.course

      Public
      Artificial Intelligence for Operations Research course
      1•7•0•0•Updated May 18, 2023May 18, 2023

    • TWAE

      Public
      A non-adversarial generative autoencoder with divide-and-conquer strategy
      Python
      •1•0•0•0•Updated Apr 18, 2023Apr 18, 2023

    • MN-PCA

      Public
      Matrix normal PCA for interpretable dimension reduction and graphical noise modeling
      MATLAB
      •0•1•0•0•Updated Feb 22, 2023Feb 22, 2023

    • SmartGate

      Public
      Jupyter Notebook
      •2•1•0•0•Updated Oct 5, 2022Oct 5, 2022

    • stagewiseNN

      Public
      Constructing developmental tree from scRNA-seq data
      Python
      •
      MIT License
      •1•3•0•0•Updated Jun 13, 2022Jun 13, 2022

    • STAGATE

      Public
      Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
      Python
      •
      MIT License
      •21•66•0•0•Updated Mar 5, 2022Mar 5, 2022

    • DeepLearningTheory.course

      Public
      Deep Learning Theory course
      4•20•0•0•Updated Jan 3, 2022Jan 3, 2022

    • scHi-CSim

      Public
      scHi-CSim, a simulator for generating single-cell Hi-C data.
      Python
      •
      MIT License
      •1•5•2•0•Updated Dec 3, 2021Dec 3, 2021

    • ADC

      Public
      source code for ADC
      Python
      •1•2•0•0•Updated Sep 16, 2021Sep 16, 2021

    • BMD-MoG

      Public
      The code file for paper BMD-MoG. main file: BMD_MoG.m
      MATLAB
      •1•0•0•0•Updated Apr 11, 2021Apr 11, 2021

    • CASAVA

      Public
      Resources of our paper CASAVA
      R
      •0•1•0•0•Updated Dec 26, 2020Dec 26, 2020

    • dbmd

      Public
      Distributed Matrix Decomposition for Big Data Mining and Clustering
      Scala
      •2•2•0•0•Updated Nov 23, 2020Nov 23, 2020

    • hicsrkit

      Public
      A package used to enhance Hi-C maps with deep learning
      0•0•0•0•Updated Sep 28, 2020Sep 28, 2020

    • DSMO.course

      Public
      Data Science and Matrix Optimization course
      course-materialsdata-sciencematrix-factorizationmanifold-learningmatrix-completionsubspace-clusteringmanifold-alignmentprecision-matrix-estimation
      37•71•0•0•Updated Sep 2, 2020Sep 2, 2020