CAST package
☆42Oct 26, 2024Updated last year
Alternatives and similar repositories for CAST
Users that are interested in CAST are comparing it to the libraries listed below
Sorting:
- Multi-slice Spatial Transcriptome Domain Analysis.☆13Dec 13, 2024Updated last year
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆39Feb 8, 2026Updated 3 weeks ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆86Nov 16, 2025Updated 3 months ago
- R package for normalisation of spatial transcriptomics data☆17Jan 21, 2026Updated last month
- A probabilistic cell typing algorithm for spatial transcriptomics.☆25Nov 6, 2025Updated 3 months ago
- Interoperability between SpatialData and the Xenium Explorer☆25Jul 31, 2024Updated last year
- Package for the analysis of Transcripts outside segmented cells in ST data☆26Updated this week
- ☆44Feb 13, 2026Updated 2 weeks ago
- ☆62Dec 8, 2025Updated 2 months ago
- cell type specific, trait-associated gene regulation☆29Mar 31, 2025Updated 11 months ago
- ☆20Updated this week
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆263Updated this week
- scTM: A package for topic modelling in transcriptomics data☆24May 1, 2024Updated last year
- Phenotype Associated Spatial Signature Analysis with Graph-based Embedding☆26Mar 5, 2025Updated 11 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆152Feb 12, 2026Updated 2 weeks ago
- MorphLink: Bridging Cellular Morphological Behaviors and Molecular Dynamics in Multi-modal Spatial Omics☆16Dec 7, 2025Updated 2 months ago
- iFISH Probe Design: a Python3 package to build iFISH probes.☆12Mar 11, 2022Updated 3 years ago
- ☆11May 24, 2024Updated last year
- Morphology-Enhanced Spatial Transcriptome Analysis Integrator☆27Mar 16, 2025Updated 11 months ago
- Test genes for Spatial Variation☆15Dec 20, 2024Updated last year
- Deep fusion of spatial transcriptomics and histology images for interpretable high-definition embedding mapping☆17Feb 4, 2026Updated 3 weeks ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆119Updated this week
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆15Updated this week
- A computational tool for identification of 3D multi-modal spatial neighborhoods☆15Aug 1, 2025Updated 7 months ago
- Minimum Information about Tissue Imaging☆21Oct 18, 2023Updated 2 years ago
- A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.☆30Jan 27, 2026Updated last month
- TCR Reconstruction Algorithm for Paired-End Single cell☆14Oct 13, 2019Updated 6 years ago
- ☆145Apr 19, 2025Updated 10 months ago
- Spatial Single-Cell Analysis Toolkit☆110Feb 20, 2026Updated last week
- Python API and Jupyter widget for Vitessce☆62Feb 12, 2026Updated 2 weeks ago
- A multi-dimensional spatial image data structure for scientific Python.☆44Aug 8, 2025Updated 6 months ago
- Image registration (alignment) software for large microscopy images☆27Oct 15, 2023Updated 2 years ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆79Updated this week
- ☆41Jan 12, 2026Updated last month
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆67Jul 2, 2025Updated 7 months ago
- Develop custom oligo design pipelines.☆27Updated this week
- Perturbation-response Score (PS) analysis is a method to quantify diverse perturbation responses and discover novel biological insights i…☆17Apr 20, 2024Updated last year
- Spatial direct messaging detected by bivariate Moran☆32Jul 16, 2025Updated 7 months ago
- An open and interoperable data framework for spatial omics data☆351Updated this week