Alternatives and similar repositories for sopa

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

• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆111Updated last month
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆70Updated 2 weeks ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆92Updated last month
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆126Updated this week
• yuqiyuqitan / SPACEc
  ☆43Updated 2 weeks ago
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆35Updated last year
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆90Updated 2 months ago
• zcang / COMMOT
  ☆118Updated last year
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆101Updated this week
• ludvb / xfuse
  Super-resolved spatial transcriptomics by deep data fusion
  ☆74Updated 2 years ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆63Updated 11 months ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆80Updated last year
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆129Updated 4 months ago
• rajewsky-lab / openst
  Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
  ☆101Updated 7 months ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆113Updated last week
• 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
• YMa-lab / CARD
  ☆120Updated last year
• azizilab / starfysh
  Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
  ☆119Updated 3 weeks ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆168Updated 11 months ago
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆62Updated 7 months ago
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆132Updated 3 months ago
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆182Updated last week
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆43Updated 11 months ago
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆289Updated this week
• fish-quant / ComSeg
  comseg
  ☆21Updated 4 months ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆62Updated last week
• rendeirolab / LazySlide
  Accessible and interoperable whole slide image analysis
  ☆94Updated last week
• drieslab / Giotto
  Spatial omics analysis toolbox
  ☆310Updated this week
• Sanofi-Public / enact-pipeline
  Repository for ENACT pipeline for end-to-end analysis of Visium HD data
  ☆52Updated last week
• kharchenkolab / Baysor
  Bayesian Segmentation of Spatial Transcriptomics Data
  ☆180Updated 6 months ago