10x Visium HD provides expression profiles for the whole transcriptome at single cell-scale resolution. The R package ctSVG implements a computational method to extract single-cell gene expression profiles from Visium HD data and identify cell-type-specific SVGs.
Beyond Visium HD data, ctSVG can also be applied broadly to other types of ST data with single-cell resolution, such as 10x Xenium.
To install the latest version of the R package from GitHub, please run following commands in R:
Sys.setenv("LIBARROW_MINIMAL" = FALSE)
Set the environment variable to install the R package arrow on Linux. More information is available at this website.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SparseArray")
if (!require("devtools"))
install.packages("devtools")
devtools::install_github("haotian-zhuang/findPC")
devtools::install_github("haotian-zhuang/ctSVG")
Detailed vignettes are available at this website.
Please cite the following paper: Haotian Zhuang, Xinyi Shang, Wenpin Hou, Zhicheng Ji. Identifying cell-type-specific spatially variable genes with ctSVG. Genome Biology (2025).
Authors: Haotian Zhuang, Zhicheng Ji
Report bugs and provide suggestions by sending email to:
Maintainer: Haotian Zhuang (haotian.zhuang@duke.edu)
Or open a new issue on this GitHub page