elixir-europe-training / ELIXIR-SCO-spatial-omicsLinks
☆45Updated 9 months ago
Alternatives and similar repositories for ELIXIR-SCO-spatial-omics
Users that are interested in ELIXIR-SCO-spatial-omics are comparing it to the libraries listed below
Sorting:
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 3 years ago
- Join subcellular Visium HD bins into cells☆131Updated 2 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆147Updated last month
- BANKSY: spatial clustering☆132Updated 2 months ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆137Updated 10 months ago
- ☆85Updated 2 weeks ago
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆71Updated 6 months ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆83Updated 9 months ago
- Direct estimation of mean and covariance from single cell RNA seq experiments☆124Updated 8 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆69Updated 2 months ago
- Significance analysis for clustering single-cell RNA-sequencing data☆124Updated last year
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆88Updated 3 weeks ago
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆89Updated 2 weeks ago
- Python implementation of Milo for differential abundance testing on KNN graph☆77Updated 10 months ago
- Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data☆151Updated 5 months ago
- A Bayesian model for compositional single-cell data analysis☆185Updated 2 years ago
- R package for semi-supervised single-cell data integration☆94Updated 3 weeks ago
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆109Updated 7 months ago
- Code used to benchmark Xenium☆73Updated last year
- Identification of persistent local patterns in spatial omics data☆14Updated 8 months ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆57Updated last month
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆87Updated 3 years ago
- ☆129Updated last year
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆80Updated 11 months ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆78Updated 3 weeks ago
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆48Updated 4 years ago
- Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…☆161Updated 2 months ago
- ☆14Updated 3 years ago
- Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data☆94Updated last month
- trajectory inference☆105Updated 11 months ago