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

Users that are interested in Deep-Learning-in-Spatial-Transcriptomics-Analysis are comparing it to the libraries listed below

• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆48Updated 4 years ago
• LiHongCSBLab / SOAPy
  ☆32Updated 10 months ago
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆73Updated 2 years ago
• dpeerlab / ENVI
  ☆52Updated 3 months ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆73Updated last year
• QihuangZhang / CeLEry
  CeLEry: cell location recovery in single-cell RNA sequencing
  ☆35Updated 10 months ago
• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆58Updated 2 years ago
• raphael-group / GASTON
  GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
  ☆69Updated last month
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆101Updated 2 months ago
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆32Updated 5 months ago
• raphael-group / paste
  Probabilistic Alignment of Spatial Transcriptomics Experiments
  ☆98Updated 10 months ago
• JiangBioLab / DeepCCI
  ☆21Updated 3 years ago
• bowang-lab / DeepVelo
  ☆47Updated last year
• prabhakarlab / Banksy_py
  BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …
  ☆72Updated last month
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆147Updated last month
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆69Updated 2 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆47Updated 2 months ago
• Banovich-Lab / Spatial_PF
  ☆34Updated 2 months ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆41Updated 10 months ago
• shuxiaoc / maxfuse
  ☆57Updated last year
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated 2 years ago
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆70Updated last year
• wanglabtongji / CCI
  Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information
  ☆23Updated 3 years ago
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆53Updated 3 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆67Updated 6 months ago
• LungCellAtlas / HLCA
  ☆66Updated 2 years ago
• LieberInstitute / spatialLIBD
  Code for the spatialLIBD R/Bioconductor package and shiny app
  ☆107Updated last month
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆77Updated 10 months ago
• wanglab-broad / CAST
  CAST package
  ☆41Updated last year
• whhudson / spatialTCR
  ☆14Updated 3 years ago