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Identification of cell-type-specific spatially variable genes accounting for excess zeros

Bioconductor version: Release (3.19)

The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS.

Author: Jinge Yu Developer [aut, cre], Xiangyu Luo Developer [aut]

Maintainer: Jinge Yu Developer <yjgruc at>

Citation (from within R, enter citation("CTSV")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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Reference Manual PDF


biocViews GeneExpression, Genetics, Regression, Software, Spatial, StatisticalMethod
Version 1.6.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License GPL-3
Depends R (>= 4.2)
Imports stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment
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Follow Installation instructions to use this package in your R session.

Source Package CTSV_1.6.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) CTSV_1.6.0.tgz
macOS Binary (arm64) CTSV_1.6.0.tgz
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Source Repository (Developer Access) git clone
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