scverse / squidpy

Related projects ⓘ

Alternatives and complementary repositories for squidpy

• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆201Updated 5 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆321Updated last month
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆236Updated this week
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆335Updated last month
• aristoteleo / spateo-release
  Spatiotemporal modeling of spatial transcriptomics
  ☆214Updated this week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆276Updated 2 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆335Updated 3 weeks ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆313Updated 5 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆297Updated 4 months ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆300Updated 5 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆188Updated this week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆313Updated last week
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆349Updated last month
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆167Updated 2 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆309Updated last month
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆259Updated 5 months ago
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆200Updated 4 months ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆218Updated 3 weeks ago
• scverse / rapids_singlecell
  Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data proces…
  ☆151Updated this week
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆418Updated last month
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆421Updated 3 weeks ago
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆201Updated this week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆382Updated 8 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆220Updated this week
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆444Updated 7 months ago
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆321Updated this week
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆166Updated 2 months ago
• Teichlab / cellphonedb
  ☆345Updated 2 years ago
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆247Updated last month
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆292Updated last month