Alternatives and similar repositories for sopa:

Users that are interested in sopa are comparing it to the libraries listed below

• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆83Updated this week
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆73Updated last month
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆31Updated 8 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆102Updated last month
• ludvb / xfuse
  Super-resolved spatial transcriptomics by deep data fusion
  ☆71Updated last year
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆45Updated this week
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆50Updated 2 years ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆42Updated 7 months ago
• zcang / COMMOT
  ☆107Updated 9 months ago
• rajewsky-lab / openst
  Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
  ☆88Updated 2 months ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆71Updated last year
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆82Updated 6 months ago
• azizilab / starfysh
  Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
  ☆108Updated 5 months ago
• yuqiyuqitan / SPACEc
  ☆23Updated this week
• kharchenkolab / Baysor
  Bayesian Segmentation of Spatial Transcriptomics Data
  ☆159Updated last month
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆35Updated 6 months ago
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆45Updated 2 years ago
• almaan / stereoscope
  Spatial mapping of cell types by integration of transcriptomics data
  ☆89Updated 2 years ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆120Updated 9 months ago
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆249Updated this week
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆79Updated 2 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆111Updated last year
• BodenmillerGroup / ImcSegmentationPipeline
  A pixel classification based multiplexed image segmentation pipeline
  ☆86Updated last year
• shuxiaoc / maxfuse
  ☆46Updated 8 months ago
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆47Updated this week
• ElementoLab / utag
  ☆33Updated 9 months ago
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆148Updated 2 weeks ago
• jfnavarro / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆70Updated this week
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆206Updated 8 months ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆52Updated this week