Tutorials for Squidpy
☆34Dec 18, 2025Updated 3 months ago
Alternatives and similar repositories for squidpy_notebooks
Users that are interested in squidpy_notebooks are comparing it to the libraries listed below
Sorting:
- Fit generalized linear models in python.☆28Mar 6, 2023Updated 3 years ago
- Spatial Single Cell Analysis in Python☆555Updated this week
- ☆22Aug 25, 2022Updated 3 years ago
- single cell analysis of treatment naive and treated human PDAC☆25May 27, 2022Updated 3 years ago
- ☆13Feb 12, 2026Updated last month
- ☆13Apr 27, 2022Updated 3 years ago
- ☆29Sep 4, 2023Updated 2 years ago
- The R Bioconductor package for scMAGeCK.☆13Apr 20, 2024Updated last year
- Multimodal Data (.h5mu) implementation for Python☆109Updated this week
- Learning cell communication from spatial graphs of cells☆113Jan 15, 2024Updated 2 years ago
- Collection of Sphinx extensions similar to (but more flexible than) numpydoc☆12Updated this week
- ☆17Mar 18, 2025Updated last year
- Dynamical systems methods for RNA velocity analysis☆24May 19, 2021Updated 4 years ago
- data and model repository for single-cell data☆136Dec 21, 2023Updated 2 years ago
- CellDrift: temporal perturbation effects for single cell data☆13Dec 3, 2022Updated 3 years ago
- Web application demonstrating 3D modeling of spatial transcriptomics☆23Dec 9, 2024Updated last year
- CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆34Jul 24, 2025Updated 7 months ago
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆67Feb 11, 2026Updated last month
- VEGA: VAE Enhanced by Gene Annotations☆17May 5, 2022Updated 3 years ago
- ☆42Mar 12, 2026Updated last week
- FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.☆13Dec 6, 2025Updated 3 months ago
- A spatial genome aligner for analyzing multiplexed DNA-FISH imaging data.☆18Oct 10, 2023Updated 2 years ago
- Alignment of spatial genomics data using deep Gaussian processes☆31Dec 14, 2022Updated 3 years ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆76Nov 13, 2025Updated 4 months ago
- Python client for the OmniPath web service☆59Feb 19, 2026Updated last month
- MCP server for single cell analysis☆12May 15, 2025Updated 10 months ago
- Computational pipeline to process EasySci-RNA data.☆23Jan 17, 2024Updated 2 years ago
- ☆13Jan 29, 2021Updated 5 years ago
- Automatically annotate cell types, consistently across samples.☆19Updated this week
- ☆13Aug 9, 2022Updated 3 years ago
- ☆12Mar 22, 2023Updated 3 years ago
- pyGPCCA - python GPCCA: Generalized Perron Cluster Cluster Analysis package to coarse-grain reversible and non-reversible Markov state mo…☆26Feb 17, 2026Updated last month
- Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Gen…☆40May 6, 2022Updated 3 years ago
- Single Cell Consensus Clustering with Speed☆21Dec 12, 2022Updated 3 years ago
- SuperCell for Cytometry data☆13Oct 14, 2025Updated 5 months ago
- software to detect doublets☆97Dec 28, 2024Updated last year
- Single-cell perturbation analysis☆295Updated this week
- A toolkit of spatial transcriptomic analysis.☆274Updated this week
- Variant impact phenotyping using Perturb-seq☆10Apr 22, 2024Updated last year