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    28 repositories

    • cellbin2

      Public
      This repository is for CellBin research group
      Python
      •
      MIT License
      •2•8•1•1•Updated Feb 5, 2025Feb 5, 2025

    • StereoSiTE

      Public
      Spatial transcriptome analysis in python
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•22•3•0•Updated Jan 26, 2025Jan 26, 2025

    • Stereopy

      Public
      A toolkit of spatial transcriptomic analysis.
      Jupyter Notebook
      •
      MIT License
      •65•216•13•0•Updated Jan 23, 2025Jan 23, 2025

    • cs-benchmark

      Public
      This repository is for cell segmentation benchmark
      PureBasic
      •
      MIT License
      •0•3•0•0•Updated Dec 23, 2024Dec 23, 2024

    • ST-GEARS

      Public
      A Spatial Transcriptomics Geospatial Profile Recovery System Tool through Anchors
      Jupyter Notebook
      •
      MIT License
      •0•14•2•0•Updated Dec 10, 2024Dec 10, 2024

    • CoDi

      Public
      Jupyter Notebook
      •0•1•2•0•Updated Nov 5, 2024Nov 5, 2024

    • SAW

      Public
      HTML
      •
      GNU General Public License v3.0
      •33•153•52•3•Updated Sep 18, 2024Sep 18, 2024

    • StereoMMv1

      Public
      StereoMM is a graph fusion model that can integrate gene expression, histological images, and spatial location. And the information interaction within modalities is strengthened by introducing an attention mechanism.
      Jupyter Notebook
      •1•30•1•0•Updated Aug 5, 2024Aug 5, 2024

    • EAGS

      Public
      EAGS:efficient and adaptive Gaussian smoothing
      Python
      •
      MIT License
      •0•6•0•0•Updated Aug 2, 2024Aug 2, 2024

    • Spatialign

      Public
      Spatially Resolved Transcriptomics Integration Algorithm
      Jupyter Notebook
      •
      MIT License
      •0•4•1•0•Updated Jul 29, 2024Jul 29, 2024

    • CellBin

      Public
      Tools for generating single-cell gene expression data
      Python
      •
      MIT License
      •3•30•11•0•Updated Jun 28, 2024Jun 28, 2024

    • geftools

      Public
      C++
      •1•2•1•0•Updated Jun 13, 2024Jun 13, 2024

    • udi

      Public
      UMI Defined Cell Segmentation Tool UDi-CST
      Python
      •0•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • gefpy

      Public
      C++
      •2•1•2•0•Updated Feb 28, 2024Feb 28, 2024

    • BatchEval

      Public
      BatchEval: An Exquisite Workflow for Evaluating Batch Effects in Data Integration
      Python
      •
      MIT License
      •0•5•0•0•Updated Feb 20, 2024Feb 20, 2024

    • VNS

      Public
      A Novel Variable Neighborhood Search Approach for Cell Clustering Using Gene Expression and Spatial Coordinates
      Python
      •
      MIT License
      •0•2•1•0•Updated Jan 22, 2024Jan 22, 2024

    • STCellbin

      Public
      Enhanced application on generating single-cell gene expression profile for high-resolution spatial transcriptomics.
      Python
      •
      MIT License
      •1•8•1•0•Updated Jan 4, 2024Jan 4, 2024

    • STOCNSFs

      Public
      STOmics Cloud Notebook Static Files
      MIT License
      •0•0•0•0•Updated Dec 22, 2023Dec 22, 2023

    • SGAE

      Public
      Jupyter Notebook
      •
      MIT License
      •1•3•0•0•Updated Dec 21, 2023Dec 21, 2023

    • SCIITensor

      Public
      Python
      •
      MIT License
      •1•5•2•0•Updated Dec 20, 2023Dec 20, 2023

    • cusingler

      Public
      Cuda
      •
      MIT License
      •0•0•0•0•Updated Nov 13, 2023Nov 13, 2023

    • StereoPath

      Public
      R
      •
      Other
      •0•1•0•0•Updated Oct 13, 2023Oct 13, 2023

    • SpatialID

      Public
      A cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding
      Python
      •
      MIT License
      •1•3•2•0•Updated Oct 12, 2023Oct 12, 2023

    • StereoTyping

      Public
      Model Training Workflow for Determining Cell Type Based on ST and IF
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 30, 2023Aug 30, 2023

    • stereoAlign

      Public
      A toolkit for data integration
      Python
      •
      MIT License
      •0•3•2•0•Updated Aug 30, 2023Aug 30, 2023

    • ST_BarcodeMap

      Public
      C++
      •
      MIT License
      •7•21•2•0•Updated Aug 2, 2023Aug 2, 2023

    • d2c

      Public
      MIT License
      •0•3•0•0•Updated Jul 5, 2023Jul 5, 2023

    • handleBam

      Public
      C++
      •0•2•0•0•Updated Apr 27, 2023Apr 27, 2023