Alternatives and similar repositories for ELIXIR-SCO-spatial-omics

Users that are interested in ELIXIR-SCO-spatial-omics are comparing it to the libraries listed below

• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆128Updated 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
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆141Updated this week
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆136Updated 8 months ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆125Updated last month
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆148Updated 3 months ago
• Sanofi-Public / enact-pipeline
  Repository for ENACT pipeline for end-to-end analysis of Visium HD data
  ☆69Updated 5 months 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 …
  ☆88Updated 8 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆169Updated 7 months ago
• YosefLab / popV
  ☆83Updated this week
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆119Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆121Updated 6 months ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆83Updated 2 years ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆180Updated 2 years ago
• Nanostring-Biostats / CosMx-Analysis-Scratch-Space
  This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…
  ☆82Updated this week
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆81Updated 7 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆168Updated 3 months ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆191Updated this week
• jtanevski / kasumi
  Identification of persistent local patterns in spatial omics data
  ☆13Updated 6 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last week
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆70Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 8 months ago
• YMa-lab / CARD
  ☆127Updated last year
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆115Updated last week
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆102Updated 5 months ago
• wagnerlab-berkeley / Compass
  ☆36Updated 7 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆90Updated 3 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆79Updated 9 months ago
• linnarsson-lab / developing-human-brain
  ☆36Updated 3 weeks ago
• Matrisome / MatrisomeAnalyzeR
  An R package for ECM molecule annotation, classification, and analysis
  ☆10Updated last year