Test genes for Spatial Variation
☆193May 7, 2024Updated 2 years ago
Alternatives and similar repositories for SpatialDE
Users that are interested in SpatialDE are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Spatially resolved transcriptomic analysis☆68Nov 17, 2022Updated 3 years ago
- Identify genes with spatial expression trends in single-cell gene expression data☆52Mar 20, 2018Updated 8 years ago
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆102Apr 30, 2026Updated 6 months ago
- Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.☆191Jan 8, 2026Updated 9 months ago
- Spatial omics analysis toolbox☆394Updated this week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Spatial Transcriptomics Capture Location Deconvolution☆216Oct 20, 2025Updated last year
- A novel machine learning pipeline to analyse spatial transcriptomics data☆262Updated this week
- SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph con…☆264Feb 9, 2026Updated 8 months ago
- Spatial alignment of single cell transcriptomic data.☆375Jul 1, 2025Updated last year
- TRAjectory-based Differential Expression analysis for SEQuencing data☆319Jun 17, 2025Updated last year
- spatial transcriptome, single cell☆77Mar 18, 2023Updated 3 years ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆465Oct 19, 2026Updated last week
- Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (ST) data☆23May 19, 2025Updated last year
- LIANA: a LIgand-receptor ANalysis frAmework☆253Aug 7, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Spatial Single Cell Analysis in Python☆612Updated this week
- nnSVG: scalable method to identify spatially variable genes (SVGs) in spatially-resolved transcriptomics data☆25Jul 14, 2026Updated 3 months ago
- A Toolbox for Spatial Transcriptomics Analysis☆172May 6, 2025Updated last year
- Code for the spatialLIBD R/Bioconductor package and shiny app☆116Oct 16, 2026Updated 2 weeks ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆272Jan 10, 2026Updated 9 months ago
- Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data☆161Aug 3, 2025Updated last year
- Spatially aware dimension reduction for spatial transcriptomics.☆70Mar 18, 2025Updated last year
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆204Aug 12, 2025Updated last year
- Single-cell Graph Cuts Optimization☆17Apr 27, 2024Updated 2 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- spatially resolved data analysis☆11Jun 10, 2022Updated 4 years ago
- Multiview Intercellular SpaTial modeling framework☆74Jan 15, 2026Updated 9 months ago
- ☆74May 28, 2025Updated last year
- Multi-sample multi-group scRNA-seq analysis tools☆248Jul 6, 2026Updated 3 months ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆492Jan 22, 2026Updated 9 months ago
- ☆24Jan 10, 2025Updated last year
- Tools and methods for analysis of single cell assay data in R☆266Oct 17, 2025Updated last year
- Interpretation of cell states using reference single-cell maps☆329Dec 19, 2025Updated 10 months ago
- Python package to perform enrichment analysis from omics data.☆301Updated this week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Learning cell communication from spatial graphs of cells☆121Jan 15, 2024Updated 2 years ago
- Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).☆92Dec 4, 2025Updated 10 months ago
- Bayesian Segmentation of Spatial Transcriptomics Data☆219Oct 2, 2026Updated 3 weeks ago
- Python library for plotting Cellphonedb results. Ported from ktplots R package.☆58Oct 12, 2026Updated 2 weeks ago
- A method for calculating single cell entropy and reconstructing cell differentiation lineage using single-cell RNA-seq data☆10May 26, 2023Updated 3 years ago
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆233Jul 2, 2026Updated 3 months ago
- NicheNet: predict active ligand-target links between interacting cells☆683Oct 23, 2026Updated last week