scverse / squidpyLinks
Spatial Single Cell Analysis in Python
☆512Updated last week
Alternatives and similar repositories for squidpy
Users that are interested in squidpy are comparing it to the libraries listed below
Sorting:
- A novel machine learning pipeline to analyse spatial transcriptomics data☆228Updated this week
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆378Updated 3 months ago
- An open and interoperable data framework for spatial omics data☆306Updated last week
- Spatial alignment of single cell transcriptomic data.☆324Updated 2 months ago
- rapids_singlecell: GPU-accelerated framework for scRNA analysis☆240Updated this week
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆369Updated last month
- CellRank: dynamics from multi-view single-cell data☆393Updated 2 weeks ago
- A tool for semi-automatic cell type classification☆405Updated this week
- Benchmarking analysis of data integration tools☆380Updated this week
- Scanpy Tutorials.☆220Updated last week
- LIANA+: an all-in-one framework for cell-cell communication☆233Updated 2 months ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆396Updated 2 months ago
- Single-cell perturbation analysis☆202Updated last week
- 🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.☆229Updated last year
- Reference mapping for single-cell genomics☆381Updated 2 months ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆431Updated 3 months ago
- Formalizing and benchmarking open problems in single-cell genomics☆395Updated last month
- Spatiotemporal modeling of spatial transcriptomics☆313Updated last month
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆473Updated 2 weeks ago
- This is the alpha version of the CellOracle package☆379Updated 8 months ago
- A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…☆215Updated 2 months ago
- A toolkit of spatial transcriptomic analysis.☆258Updated last week
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆226Updated last week
- tools and notes for spatial omics☆314Updated 6 months ago
- Spatial omics analysis toolbox☆319Updated last week
- muon is a multimodal omics Python framework☆247Updated last month
- Python package to perform enrichment analysis from omics data.☆223Updated last week
- Single cell perturbation prediction☆315Updated 9 months ago
- scripts and notebooks from sanbomics☆442Updated 9 months ago
- Annotated data.☆656Updated last week