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ctSVG

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.

Installation

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")

Vignettes

Detailed vignettes are available at this website.

Citation

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).

Contact

Authors: Haotian Zhuang, Zhicheng Ji

Report bugs and provide suggestions by sending email to:

Maintainer: Haotian Zhuang ()

Or open a new issue on this GitHub page