tpSVG

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see tpSVG.

Thin plate models to detect spatially variable genes

Bioconductor version: 3.19

The goal of `tpSVG` is to detect and visualize spatial variation in the gene expression for spatially resolved transcriptomics data analysis. Specifically, `tpSVG` introduces a family of count-based models, with generalizable parametric assumptions such as Poisson distribution or negative binomial distribution. In addition, comparing to currently available count-based model for spatially resolved data analysis, the `tpSVG` models improves computational time, and hence greatly improves the applicability of count-based models in SRT data analysis.

Author: Boyi Guo [aut, cre] , Lukas M. Weber [ctb] , Stephanie C. Hicks [aut]

Maintainer: Boyi Guo <boyi.guo.work at gmail.com>

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

Installation

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


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

BiocManager::install("tpSVG")

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("tpSVG")

intro_to_tpSVG	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DimensionReduction, GeneExpression, Preprocessing, Regression, Software, Spatial, StatisticalMethod, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.19 (R-4.4) (< 6 months)
License	MIT + file LICENSE
Depends	mgcv, R (>= 4.4)
Imports	stats, BiocParallel, MatrixGenerics, methods, SingleCellExperiment, SummarizedExperiment, SpatialExperiment
System Requirements
URL	https://github.com/boyiguo1/tpSVG
Bug Reports	https://github.com/boyiguo1/tpSVG/issues

Suggests	BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0)
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	tpSVG_1.0.0.tar.gz
Windows Binary (x86_64)	tpSVG_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	tpSVG_1.0.0.tgz
macOS Binary (arm64)	tpSVG_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tpSVG
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tpSVG
Bioc Package Browser	https://code.bioconductor.org/browse/tpSVG/
Package Short Url	https://bioconductor.org/packages/tpSVG/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.19	Source Archive