Alternatives and similar repositories for SPACEc

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

• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆133Updated last week
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆89Updated last year
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆139Updated last week
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆41Updated last week
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆126Updated this week
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆99Updated 3 months ago
• rajewsky-lab / openst
  Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
  ☆106Updated 3 months ago
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆37Updated last year
• dpeerlab / ENVI
  ☆50Updated 2 weeks ago
• shuxiaoc / maxfuse
  ☆56Updated last year
• seqscope / ficture
  ☆38Updated 2 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆44Updated 3 weeks ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆39Updated 7 months ago
• prabhakarlab / Banksy_py
  ☆64Updated 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
• raphael-group / GASTON
  GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
  ☆61Updated 4 months ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆69Updated last year
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆65Updated 3 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆84Updated 3 months ago
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆61Updated last month
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆77Updated 2 weeks ago
• gustaveroussy / sopa
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…
  ☆238Updated this week
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆67Updated 11 months ago
• Feanor007 / MESA
  A python package for Multiomics and Ecological Spatial Analysis (MESA)
  ☆21Updated 6 months ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆124Updated last week
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆27Updated last year
• almaan / stereoscope
  Spatial mapping of cell types by integration of transcriptomics data
  ☆95Updated 3 years ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆46Updated 4 years 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 …
  ☆87Updated 7 months ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆133Updated 8 months ago