almaan / stereoscope
Spatial mapping of cell types by integration of transcriptomics data
☆91Updated 2 years ago
Alternatives and similar repositories for stereoscope:
Users that are interested in stereoscope are comparing it to the libraries listed below
- ☆118Updated 3 years ago
- Join subcellular Visium HD bins into cells☆93Updated 4 months ago
- BANKSY: spatial clustering☆105Updated last month
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆124Updated 2 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆118Updated 3 weeks ago
- A tool for semi-automatic cell type harmonization and integration☆102Updated last month
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 2 years ago
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆60Updated last month
- ☆116Updated last year
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆43Updated last week
- STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)☆100Updated last year
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆79Updated last month
- Methods to compute Local Inverse Simpson's Index (LISI)☆61Updated 3 years ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆60Updated 10 months ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆143Updated 3 months ago
- Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…☆39Updated 3 years ago
- Python implementation of Milo for differential abundance testing on KNN graph☆67Updated 2 months ago
- Methods to discover gene programs on single-cell data☆113Updated last month
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆63Updated 2 years ago
- This repository contains all code used for the Human Lung Cell Atlas project.☆49Updated last year
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆40Updated 3 years ago
- ☆114Updated last year
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆72Updated 5 months ago
- Code used to benchmark Xenium☆57Updated 9 months ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆158Updated 3 weeks ago
- Construct Tumor Transition Zone Microenvironment☆42Updated 5 months ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆52Updated 7 months ago
- Single-cell Lung Cancer Atlas with 1.2M cells☆62Updated 3 months ago
- Single-Cell Clustering Assessment Framework☆101Updated last year
- Metacells - Single-cell RNA Sequencing Analysis☆104Updated 6 months ago