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nnSVG

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


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics
Version 1.6.0
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
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Depends On Me
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Package Archives

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

Source Package nnSVG_1.6.0.tar.gz
Windows Binary nnSVG_1.6.0.zip (64-bit only)
macOS Binary (x86_64) nnSVG_1.6.0.tgz
macOS Binary (arm64) nnSVG_1.6.0.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