nnSVG
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
Bioconductor version: Release (3.19)
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.
Author: Lukas M. Weber [aut, cre] 
, Stephanie C. Hicks [aut]
Maintainer: Lukas M. Weber <lmweberedu at gmail.com>
citation("nnSVG")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("nnSVG")
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("nnSVG")| nnSVG Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.2) |
| Imports | SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods |
| System Requirements | |
| URL | https://github.com/lmweber/nnSVG |
| Bug Reports | https://github.com/lmweber/nnSVG/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | spoon |
| Suggests Me | tpSVG |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | nnSVG_1.8.0.tar.gz |
| Windows Binary (x86_64) | nnSVG_1.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | nnSVG_1.8.0.tgz |
| macOS Binary (arm64) | nnSVG_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/nnSVG |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/nnSVG |
| Bioc Package Browser | https://code.bioconductor.org/browse/nnSVG/ |
| Package Short Url | https://bioconductor.org/packages/nnSVG/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |