elixir-europe-training / ELIXIR-SCO-spatial-omicsLinks
☆39Updated 3 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:
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆53Updated last month
- Join subcellular Visium HD bins into cells☆112Updated last month
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 3 years ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆131Updated 4 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆126Updated 2 weeks ago
- BANKSY: spatial clustering☆117Updated 2 weeks ago
- ☆79Updated this week
- Python implementation of Milo for differential abundance testing on KNN graph☆72Updated 4 months ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆164Updated 3 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆61Updated last week
- Direct estimation of mean and covariance from single cell RNA seq experiments☆110Updated 2 months ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆77Updated 3 months ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆74Updated 5 months ago
- ☆53Updated last year
- Probabilistic cell segmentation for in situ spatial transcriptomics☆105Updated this week
- Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration☆101Updated last week
- Significance analysis for clustering single-cell RNA-sequencing data☆116Updated 10 months ago
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆63Updated last week
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆54Updated 2 months ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆74Updated 2 years ago
- Code used to benchmark Xenium☆64Updated last year
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆71Updated this week
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆85Updated 4 months ago
- Identification of spatial homogeneous regions☆21Updated 5 months ago
- A Bayesian model for compositional single-cell data analysis☆169Updated 2 years ago
- Gene group activity utility functions for Scanpy☆79Updated 6 months ago
- R package for semi-supervised single-cell data integration☆83Updated last month
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆113Updated last year
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆84Updated last month
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆43Updated 3 years ago