tpSVG

Thin plate models to detect spatially variable genes


Bioconductor version: Release (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

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
See More
Suggests BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0)
Linking To
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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