SindiLab / Deep-Learning-in-Spatial-Transcriptomics-Analysis

Related projects ⓘ

Alternatives and complementary repositories for Deep-Learning-in-Spatial-Transcriptomics-Analysis

• LiHongCSBLab / SOAPy
  ☆12Updated 3 weeks ago
• snap-stanford / stellar
  ☆61Updated last year
• QihuangZhang / CeLEry
  CeLEry: cell location recovery in single-cell RNA sequencing
  ☆31Updated 6 months ago
• MICS-Lab / novae
  Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…
  ☆23Updated last month
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆38Updated 3 years ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆49Updated 5 months ago
• YangLabHKUST / STitch3D
  Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
  ☆56Updated 11 months ago
• theislab / scArches-reproducibility
  Reproducing result from the paper
  ☆33Updated 3 years ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆40Updated 4 months ago
• romain-lopez / DestVI-reproducibility
  Reproducing the experiments of the DestVI paper
  ☆17Updated 2 years ago
• dpeerlab / ENVI
  ☆37Updated 3 weeks ago
• BiomedicalMachineLearning / Spacell
  ☆25Updated 4 years ago
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆64Updated last year
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆68Updated 10 months ago
• shuxiaoc / mario-py
  MARIO: single-cell proteomic data matching and integration using both shared and distinct features
  ☆21Updated last year
• AI4SCR / ATHENA
  ☆31Updated 3 weeks ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆85Updated last week
• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆44Updated last year
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆24Updated 6 months ago
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆51Updated this week
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆58Updated 2 years ago
• theislab / scTab
  ☆44Updated last month
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated last year
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆36Updated 2 months ago
• dchary / ucdeconvolve
  UniCell Deconvolve - Cloud Cell Type Deconvolution For Transcriptomic Data
  ☆20Updated last year
• theislab / prophet
  ☆25Updated 2 months ago
• Mr-Milk / SpatialTis
  Spatial analysis toolkit for single cell multiplexed tissue data
  ☆30Updated 2 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆56Updated 4 months ago
• welch-lab / cytosignal
  ☆16Updated 2 weeks ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆52Updated this week