CSOgroup / cellcharter
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
☆110Updated 2 weeks ago
Alternatives and similar repositories for cellcharter:
Users that are interested in cellcharter are comparing it to the libraries listed below
- Join subcellular Visium HD bins into cells☆85Updated 3 months ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆125Updated last month
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 2 years ago
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆75Updated 2 weeks ago
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆57Updated 4 months ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆75Updated last year
- Code used to benchmark Xenium☆51Updated 8 months ago
- Spatial mapping of cell types by integration of transcriptomics data☆90Updated 2 years ago
- BANKSY: spatial clustering☆94Updated 2 weeks ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆59Updated 9 months ago
- Python implementation of Milo for differential abundance testing on KNN graph☆63Updated last month
- Single-Cell Clustering Assessment Framework☆99Updated last year
- Spatial Single-Cell Analysis Toolkit☆86Updated last month
- trajectory inference☆97Updated last month
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆61Updated 6 months ago
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆40Updated 3 years ago
- ☆110Updated 10 months ago
- Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology☆111Updated 7 months ago
- ☆29Updated last month
- Bayesian Analytics for Spatial Segmentation☆25Updated 5 months ago
- ☆115Updated 2 years ago
- ☆45Updated last week
- ☆42Updated 3 months ago
- ☆71Updated last week
- Metacells - Single-cell RNA Sequencing Analysis☆103Updated 5 months ago
- Single-cell Lung Cancer Atlas with 1.2M cells☆60Updated 2 months ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆33Updated 10 months ago
- Direct estimation of mean and covariance from single cell RNA seq experiments☆100Updated last month
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆52Updated last month
- A tool for semi-automatic cell type harmonization and integration☆102Updated last year