Cottrazm: Construct Tumor Transition Zone (Boundary) Microenvironment based on spatial transcriptomics

Overview

Cottrazm (Construct Tumor Transition Zone (Boundary) Microenvironment based on spatial transcriptomics) aims to construct the microenvironment of tumor boundary based on spatial transcriptomics, single-cell transcriptomics and HE-stained histological images. It consists of three core functions: determining the tumor boundary (Cottrazm-BoundaryDefine), deconvoluting spatial transcriptomics (Cottrazm-SpatialDecon), and reconstructing a spatial gene expression matrix for sub-spots (Cottrazm-SpatialRecon).

Taken together, Cottrazm provides an integrated tool framework to dissect the tumor spatial microenvironment and facilitates the discovery of functional biological insights, thereby identifying therapeutic targets in oncologic ST datasets.

Installation

The development version can be installed from git hub with 'devtools'.

# Install devtools, if necessary
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

devtools::install_github("Yelab2020/Cottrazm")

You can also download Cottrazm through docker. Make sure you have docker installed.

docker pull skye12138/cottrazm:latest

Usage

For usage of Cottrazm, please refer to the vignette

How to cite Cottrazm

Please cite the following manuscript: Xun, Z., Ding, X., Zhang, Y. et al. Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis. Nat Commun 14, 933 (2023). https://doi.org/10.1038/s41467-023-36560-7