nnSVG

This is the released version of nnSVG; for the devel version, see nnSVG.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

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

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-3282-1730 , Stephanie C. Hicks [aut] ORCID: 0000-0002-7858-0231

Maintainer: Lukas M. Weber <weberlm3 at gmail.com>

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 1.16.1, https://bioconductor.org/packages/nnSVG.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics
Version	1.16.1
In Bioconductor since	BioC 3.15 (R-4.2) (4.5 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

Suggests	BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat
Linking To
Enhances
Depends On Me
Imports Me	OSTA, spoon
Suggests Me	SEraster, tpSVG
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	nnSVG_1.16.1.tar.gz
Windows Binary (x86_64)	nnSVG_1.16.1.zip
macOS Binary (big-sur-x86_64)	nnSVG_1.16.1.tgz
macOS Binary (sonoma-arm64)	nnSVG_1.16.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/nnSVG
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/nnSVG
Package Short Url	https://bioconductor.org/packages/nnSVG/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive