CTSV
Identification of cell-type-specific spatially variable genes accounting for excess zeros
Bioconductor version: Release (3.20)
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("CTSV")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Genetics, Regression, Software, Spatial, StatisticalMethod |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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 |
See More
| Suggests | testthat, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CTSV_1.8.0.tar.gz |
| Windows Binary (x86_64) | CTSV_1.8.0.zip |
| macOS Binary (x86_64) | CTSV_1.8.0.tgz |
| macOS Binary (arm64) | CTSV_1.8.0.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 |