nnSVG
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
Bioconductor version: 3.24 · Package version: 1.17.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("nnSVG")Details
| Maintainer | Lukas M. Weber <weberlm3@gmail.com> |
| Author | Lukas M. Weber [aut, cre] (ORCID: <https://orcid.org/0000-0002-3282-1730>), Stephanie C. Hicks [aut] (ORCID: <https://orcid.org/0000-0002-7858-0231>) |
| License | MIT + file LICENSE |
| URL | https://github.com/lmweber/nnSVG |
| Bug Reports | https://github.com/lmweber/nnSVG/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/nnSVG/ |
Citation
From within R, enter citation("nnSVG"):
Lukas M. Weber, Stephanie C. Hicks. nnSVG: Scalable identification of spatially variable genes in spatially-resolved transcriptomics data. doi:10.18129/B9.bioc.nnSVG, R package version 1.17.1, https://bioconductor.org/packages/nnSVG.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | nnSVG_1.17.1.tar.gz |
| Windows binary (x86_64) | nnSVG_1.17.1.zip |
| macOS binary (arm64) | nnSVG_1.17.1.tgz |
| macOS binary (x86_64) | nnSVG_1.17.1.tgz |
Dependencies
Depends: R (>= 4.2)
Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods
Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat