BiomedicalMachineLearning / stLearn
A novel machine learning pipeline to analyse spatial transcriptomics data
☆208Updated 9 months ago
Alternatives and similar repositories for stLearn:
Users that are interested in stLearn are comparing it to the libraries listed below
- LIANA+: an all-in-one framework for cell-cell communication☆190Updated last month
- Perturbation Analysis in the scverse ecosystem.☆160Updated last week
- Benchmarking analysis of data integration tools☆337Updated 2 months ago
- A tool for semi-automatic cell type classification☆342Updated 2 months ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆205Updated last month
- Spatial omics analysis toolbox☆284Updated this week
- Episcanpy: Epigenomics Single Cell Analysis in Python☆142Updated 3 months ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆343Updated 9 months ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆313Updated last week
- Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.☆129Updated 2 years ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆140Updated 2 months ago
- 🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.☆217Updated 8 months ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆123Updated 3 weeks ago
- Reference mapping for single-cell genomics☆355Updated 2 weeks ago
- Test genes for Spatial Variation☆160Updated 10 months ago
- Python package to perform enrichment analysis from omics data.☆181Updated last month
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆340Updated last week
- Spatial Transcriptomics Capture Location Deconvolution☆172Updated last year
- A package to help convert different single-cell data formats to each other☆409Updated last year
- Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data proces…☆176Updated this week
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆225Updated last year
- Batch balanced KNN☆154Updated last year
- Spatial alignment of single cell transcriptomic data.☆278Updated 9 months ago
- Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.☆145Updated this week
- Scissor package☆208Updated 10 months ago
- A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…☆178Updated 3 weeks ago
- A toolkit of spatial transcriptomic analysis.☆223Updated last week
- LIANA: a LIgand-receptor ANalysis frAmework☆196Updated 7 months ago
- Detect doublets in single-cell RNA-seq data☆143Updated 4 years ago
- EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.☆197Updated 11 months ago