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CTSV

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


Bioconductor version: Release (3.18)

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 ruc.edu.cn>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CTSV")

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

Documentation

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

browseVignettes("CTSV")
Basic Usage HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Genetics, Regression, Software, Spatial, StatisticalMethod
Version 1.4.0
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
System Requirements
URL https://github.com/jingeyu/CTSV
Bug Reports https://github.com/jingeyu/CTSV/issues
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CTSV_1.4.0.tar.gz
Windows Binary CTSV_1.4.0.zip (64-bit only)
macOS Binary (x86_64) CTSV_1.4.0.tgz
macOS Binary (arm64) CTSV_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CTSV
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CTSV
Bioc Package Browser https://code.bioconductor.org/browse/CTSV/
Package Short Url https://bioconductor.org/packages/CTSV/
Package Downloads Report Download Stats