BodenmillerGroup / cytomapper
R package for visualization of highly multiplexed imaging data
☆32Updated 9 months ago
Alternatives and similar repositories for cytomapper:
Users that are interested in cytomapper are comparing it to the libraries listed below
- R based workflow for multiplexed imaging data☆31Updated last year
- A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.☆61Updated 6 months ago
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆10Updated 2 years ago
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆14Updated 3 years ago
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆57Updated 5 months ago
- ☆28Updated 6 months ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆35Updated 11 months ago
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆52Updated 10 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆115Updated 2 weeks ago
- ☆26Updated 6 months ago
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆72Updated 2 years ago
- An R package for handling and analysing imaging mass cytometry data☆24Updated 5 months ago
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆45Updated 2 years ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆37Updated last year
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆27Updated 6 months ago
- Tools to handle IMC data☆23Updated 3 years ago
- Spatial Single-Cell Analysis Toolkit☆91Updated 3 weeks ago
- Helper functions for working with inForm data.☆14Updated 2 years ago
- Segmentation error aware clustering for multiplexed imaging☆17Updated 3 months ago
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆59Updated 3 weeks ago
- A pixel classification based multiplexed image segmentation pipeline☆93Updated last year
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆77Updated last year
- Histology Topography Cytometry Analysis Toolbox☆67Updated last year
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆62Updated this week
- CellProfiler plugins for multiplexed image analysis☆12Updated 4 years ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆68Updated this week
- The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…☆38Updated 4 months ago
- ☆50Updated 7 years ago
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 2 years ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆52Updated 6 months ago