CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

tools and notes for spatial omics

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data

Spatial Transcriptomics Dashboard

Deep Learning Library for Single Cell Analysis

napari: a fast, interactive, multi-dimensional image viewer for python

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

A sleek, highly customizable timer for speedrunners.

Publication-ready volcano plots with enhanced colouring and labeling

Spatial Single Cell Analysis in Python

A project - tutorial. Differential expression of RNAseq raw counts data using a Real world dataset in R. Packages covered 'DESeq2' and 'EnhancedVolcano'

Annotated data.

Dockerized multi-channel image processing framework

Fiji library to perform image segmentation based on the Weka learning schemes

Test data to be used for automated testing with the nf-core pipelines

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.

A pixel classification based multiplexed image segmentation pipeline

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

Core classes and components used by CellProfiler

Visualization of highly multiplexed imaging data

ExperimentHub collection of imaging mass cytometry datasets

Community-contributed and experimental CellProfiler modules.

This repository hosts an R based workflow to perform downstream analysis of IMC data.

An R package for handling and analysing imaging mass cytometry data

Tutorials for Squidpy

Image Mass Cytometry analysis pipeline

Dimensionality reduction (UMAP, t-SNE, PCA) for ImageJ/Fiji