BiomedicalMachineLearning / stLearnLinks
A novel machine learning pipeline to analyse spatial transcriptomics data
☆234Updated 2 weeks ago
Alternatives and similar repositories for stLearn
Users that are interested in stLearn are comparing it to the libraries listed below
Sorting:
- LIANA+: an all-in-one framework for cell-cell communication☆243Updated 3 weeks ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆386Updated last month
- Python package to perform enrichment analysis from omics data.☆238Updated this week
- A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…☆223Updated 4 months ago
- 🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.☆241Updated last year
- Single-cell perturbation analysis☆212Updated last week
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆141Updated this week
- Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.☆177Updated last week
- Spatial alignment of single cell transcriptomic data.☆333Updated 4 months ago
- Batch balanced KNN☆174Updated 2 years ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆384Updated 2 months ago
- Spatial Transcriptomics Capture Location Deconvolution☆196Updated 3 weeks ago
- ☆124Updated last year
- Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.☆143Updated 2 years ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆136Updated 8 months ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆407Updated 3 months ago
- Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms☆178Updated last year
- Scanpy Tutorials.☆228Updated this week
- Episcanpy: Epigenomics Single Cell Analysis in Python☆148Updated 11 months ago
- Benchmarking analysis of data integration tools☆392Updated last month
- Code for the spatialLIBD R/Bioconductor package and shiny app☆102Updated last week
- Join subcellular Visium HD bins into cells☆128Updated last week
- Test genes for Spatial Variation☆175Updated last year
- EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.☆218Updated last year
- A tool for semi-automatic cell type classification☆424Updated last week
- A toolkit of spatial transcriptomic analysis.☆265Updated 3 weeks ago
- ☆124Updated 3 years ago
- rapids_singlecell: GPU-accelerated framework for scRNA analysis☆261Updated this week
- Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology☆123Updated 5 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆242Updated last week