A novel machine learning pipeline to analyse spatial transcriptomics data
☆242Mar 12, 2026Updated last week
Alternatives and similar repositories for stLearn
Users that are interested in stLearn are comparing it to the libraries listed below
Sorting:
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆422Updated this week
- ☆33Feb 25, 2025Updated last year
- Spatial Transcriptomics Capture Location Deconvolution☆203Oct 20, 2025Updated 4 months ago
- Spatial alignment of single cell transcriptomic data.☆358Jul 1, 2025Updated 8 months ago
- Spatial Single Cell Analysis in Python☆555Updated this week
- Spatially resolved transcriptomic analysis☆64Nov 17, 2022Updated 3 years ago
- Spatial omics analysis toolbox☆362Feb 12, 2026Updated last month
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆444Jan 22, 2026Updated last month
- Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.☆169Jan 8, 2026Updated 2 months ago
- A toolkit of spatial transcriptomic analysis.☆274Feb 12, 2026Updated last month
- Spatiotemporal modeling of spatial transcriptomics☆330Feb 25, 2026Updated 3 weeks ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆138Feb 20, 2025Updated last year
- SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph con…☆257Feb 9, 2026Updated last month
- Identify spatial domain☆90May 29, 2025Updated 9 months ago
- Spatial Single-Cell Analysis Toolkit☆110Mar 11, 2026Updated last week
- ☆128Mar 27, 2022Updated 3 years ago
- BANKSY: spatial clustering☆137Oct 15, 2025Updated 5 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆158Mar 9, 2026Updated last week
- STRIDE (Spatial TRanscRIptomics DEconvolution by topic modelling) is a cell-type deconvolution tool for spatial transcriptomics by using …☆27Jan 23, 2024Updated 2 years ago
- A Toolbox for Spatial Transcriptomics Analysis☆166May 6, 2025Updated 10 months ago
- CellRank: dynamics from multi-view single-cell data☆433Mar 9, 2026Updated last week
- ☆145Apr 19, 2025Updated 11 months ago
- Test genes for Spatial Variation☆183May 7, 2024Updated last year
- LIANA: a LIgand-receptor ANalysis frAmework☆234Aug 7, 2024Updated last year
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆75Nov 13, 2025Updated 4 months ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆470Jun 6, 2025Updated 9 months ago
- Gene group activity utility functions for Scanpy☆100Dec 21, 2024Updated last year
- Interactive applications of stlearn☆15May 1, 2023Updated 2 years ago
- Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics☆82Mar 5, 2022Updated 4 years ago
- A tool for semi-automatic cell type classification☆459Mar 13, 2026Updated last week
- Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data☆74Jan 17, 2025Updated last year
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆95Dec 11, 2023Updated 2 years ago
- Interpretation of cell states using reference single-cell maps☆313Dec 19, 2025Updated 3 months ago
- Bayesian Segmentation of Spatial Transcriptomics Data☆202Dec 10, 2024Updated last year
- Multiview Intercellular SpaTial modeling framework☆72Jan 15, 2026Updated 2 months ago
- ☆148Mar 19, 2024Updated 2 years ago
- ☆31Aug 2, 2023Updated 2 years ago
- Code for the spatialLIBD R/Bioconductor package and shiny app☆111Jan 15, 2026Updated 2 months ago
- Identify genes with spatial expression trends in single-cell gene expression data☆51Mar 20, 2018Updated 7 years ago