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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | tpSVG_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | tpSVG_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | tpSVG_1.9.0.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 |