Repositories list

• cellbin2

  Public
  This repository is for CellBin research group

  Python

  •

  MIT License

  •2•9•1•1•Updated Mar 4, 2025Mar 4, 2025

• stereo3d

  Public
  Python

  •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

• Stereopy

  Public
  A toolkit of spatial transcriptomic analysis.

  Jupyter Notebook

  •

  MIT License

  •67•222•10•2•Updated Feb 24, 2025Feb 24, 2025

• SpatialID

  Public
  A cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding

  Python

  •

  MIT License

  •1•3•2•0•Updated Feb 21, 2025Feb 21, 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

• cs-benchmark

  Public
  This repository is for cell segmentation benchmark

  PureBasic

  •

  MIT License

  •0•4•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•154•55•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•31•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•31•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•9•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

• 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•3•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