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("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 | ||
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 | |
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 | 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 |