R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma".
☆17Sep 26, 2021Updated 4 years ago
Alternatives and similar repositories for SpatialScore
Users that are interested in SpatialScore are comparing it to the libraries listed below
Sorting:
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆11Mar 3, 2023Updated 2 years ago
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆71Nov 4, 2024Updated last year
- ☆18Apr 5, 2024Updated last year
- MARIO: single-cell proteomic data matching and integration using both shared and distinct features☆22Jan 9, 2026Updated last month
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆52May 20, 2022Updated 3 years ago
- A computational tool for identification of 3D multi-modal spatial neighborhoods☆15Aug 1, 2025Updated 6 months ago
- Spatial RNA velocity☆10Oct 3, 2024Updated last year
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆39May 7, 2024Updated last year
- Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.☆23Jan 22, 2026Updated last month
- ☆19Apr 8, 2025Updated 10 months ago
- ☆71May 28, 2025Updated 8 months ago
- The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…☆41Feb 5, 2026Updated 3 weeks ago
- QuPath extension for Cellsparse☆19May 6, 2025Updated 9 months ago
- Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.…☆47Sep 29, 2025Updated 4 months ago
- Create web-based OME-Zarr galleries☆22Nov 6, 2025Updated 3 months ago
- Foundation of vector-like and list-like containers in Bioconductor☆17Oct 30, 2025Updated 3 months ago
- ☆33Oct 10, 2025Updated 4 months ago
- Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari☆28Updated this week
- ☆24Oct 10, 2025Updated 4 months ago
- ☆24Jun 6, 2023Updated 2 years ago
- ImgLib2 RealTransform brought to QuPath☆29Oct 1, 2025Updated 4 months ago
- ☆31Jun 10, 2025Updated 8 months ago
- Spatial Single-Cell Analysis Toolkit☆110Feb 20, 2026Updated last week
- QuPath extension to work with WSInfer - https://wsinfer.readthedocs.io/☆28Dec 3, 2025Updated 2 months ago
- Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper☆27Nov 21, 2022Updated 3 years ago
- an SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT da…☆26Mar 11, 2025Updated 11 months ago
- The Single-Cell Pathology Landscape of Breast Cancer☆27Jan 14, 2020Updated 6 years ago
- VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:☆34Apr 17, 2023Updated 2 years ago
- ☆31May 4, 2025Updated 9 months ago
- Code for the identification step for CSI-Microbes☆31Nov 25, 2024Updated last year
- A repository for benchmarking spatial deconvolution and mapping tools☆36May 13, 2025Updated 9 months ago
- NGFF-Converter is a GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF☆35Nov 26, 2025Updated 3 months ago
- ☆71Jan 18, 2023Updated 3 years ago
- SPATA Package for spatial gene expression analysis☆21May 6, 2022Updated 3 years ago
- Computer simulator of multiplex tissue images from a set of user-defined parameters☆10Dec 13, 2022Updated 3 years ago
- ImageJ / Fiji macro to automatically export Leica LIF file as individual images (batch mode available)☆11Feb 15, 2022Updated 4 years ago
- Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles☆33Apr 4, 2025Updated 10 months ago
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.☆31May 27, 2025Updated 9 months ago
- OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning …☆35Jan 16, 2026Updated last month