Cottrazm: Construct Tumor Transition Zone (Boundary) Microenvironment based on spatial transcriptomics
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.
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")
For usage of Cottrazm, please refer to the vignette