CTSV

DOI: 10.18129/B9.bioc.CTSV  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Basic Usage
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Genetics, Regression, Software, Spatial, StatisticalMethod
Version	1.0.0
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_1.0.0.tar.gz
Windows Binary	CTSV_1.0.0.zip
macOS Binary (x86_64)	CTSV_1.0.0.tgz
macOS Binary (arm64)	CTSV_1.0.0.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