nnSVG

DOI: 10.18129/B9.bioc.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 (3.16)

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>

Citation (from within R, enter citation("nnSVG")):

Installation

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

 

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

Details

biocViews GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics
Version 1.1.13
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
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_1.1.13.tar.gz
Windows Binary nnSVG_1.1.13.zip
macOS 10.13 (High Sierra) nnSVG_1.1.13.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: