Alternatives and similar repositories for squidpy

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

• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆374Updated 2 months ago
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆227Updated last month
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆302Updated this week
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆234Updated this week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆364Updated last week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆400Updated this week
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆318Updated 2 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆393Updated 4 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆220Updated last week
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆374Updated 7 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆391Updated last month
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆227Updated last month
• aristoteleo / spateo-release
  Spatiotemporal modeling of spatial transcriptomics
  ☆310Updated last month
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆382Updated last month
• scverse / pertpy
  Single-cell perturbation analysis
  ☆200Updated this week
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆422Updated 2 months ago
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆386Updated 2 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆375Updated 7 months ago
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆224Updated last year
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆221Updated last week
• theislab / scgen
  Single cell perturbation prediction
  ☆315Updated 8 months ago
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆258Updated 2 months ago
• scverse / anndata
  Annotated data.
  ☆651Updated this week
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆470Updated 2 weeks ago
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆214Updated 2 months ago
• gustaveroussy / sopa
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…
  ☆222Updated this week
• scverse / muon
  muon is a multimodal omics Python framework
  ☆245Updated 2 weeks ago
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆313Updated 6 months ago
• drieslab / Giotto
  Spatial omics analysis toolbox
  ☆316Updated last week
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆438Updated 9 months ago