Pigeongeon

Giotto

Spatial omics analysis toolbox

LUAD-Spatial

Spatial omics analysis of human LUAD by Visium and PhenoCycler

NeighborhoodCoordination

Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front"

phenomenalist

Analysis Toolkit for PhenoCycler (CODEX) Data in R

scPROTEIN

sopa

Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

spatial-bonemarrow-atlas

This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Proteomic Profiling Reveals the Cellular Composition and Spatial Organization of the Human Bone Marrow Microenvironment"

Spatial-insights-into-immunotherapy-response

spatial_mulitplex_immunofluorescence

Code to analyze spatial multiplex immunofluorescence data (CODEX/phenocycler)

Spatial_small_intestine

Code for CODEX data

SpatialScore

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".

omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

scGPT