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nnSVG

This is the development version of nnSVG; for the stable release version, see nnSVG.

Scalable identification of spatially variable genes in spatially-resolved transcriptomics data


Bioconductor version: Development (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 (from within R, enter citation("nnSVG")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF

Details

biocViews GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics
Version 1.7.4
In Bioconductor since BioC 3.15 (R-4.2) (2 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_1.7.4.tar.gz
Windows Binary
macOS Binary (x86_64) nnSVG_1.7.4.tgz
macOS Binary (arm64)
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