CTSV

DOI: 10.18129/B9.bioc.CTSV    

This is the development version of CTSV; for the stable release version, see CTSV.

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

Bioconductor version: Development (3.17)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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Details

biocViews GeneExpression, Genetics, Regression, Software, Spatial, StatisticalMethod
Version 1.1.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License GPL-3
Depends R (>= 4.2)
Imports stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment
LinkingTo
Suggests testthat, BiocStyle
SystemRequirements
Enhances
URL https://github.com/jingeyu/CTSV
BugReports https://github.com/jingeyu/CTSV/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package CTSV_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CTSV
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CTSV
Package Short Url https://bioconductor.org/packages/CTSV/
Package Downloads Report Download Stats

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