tpSVG
This is the development version of tpSVG; for the stable release version, see tpSVG.
Thin plate models to detect spatially variable genes
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Boyi Guo <boyi.guo.work at gmail.com>
citation("tpSVG")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DimensionReduction, GeneExpression, Preprocessing, Regression, Software, Spatial, StatisticalMethod, Transcriptomics |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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 | |
| 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | tpSVG_1.3.0.zip (64-bit only) |
| macOS Binary (x86_64) | tpSVG_1.3.0.tgz |
| macOS Binary (arm64) | |
| 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 |