nnSVG

DOI: 10.18129/B9.bioc.nnSVG  

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

Bioconductor version: Release (3.16)

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 <lukas.weber.edu at gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	nnSVG tutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.2)
Imports	SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, STexampleData, scran, ggplot2, testthat
SystemRequirements
Enhances
URL	https://github.com/lmweber/nnSVG
BugReports	https://github.com/lmweber/nnSVG/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	nnSVG_1.2.0.tar.gz
Windows Binary	nnSVG_1.2.0.zip
macOS Binary (x86_64)	nnSVG_1.2.0.tgz
macOS Binary (arm64)	nnSVG_1.2.0.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