nnSVG
This is thereleased version of nnSVG; for the devel version, seennSVG.
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
Bioconductor version: Release (3.22)
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 <lmweb012 at gmail.com>
citation("nnSVG")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("nnSVG")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression,Preprocessing,SingleCell,Software,Spatial,Transcriptomics |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 years) |
| License | MIT + fileLICENSE |
| 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, OSTA |
| Suggests Me | SEraster,tpSVG |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | nnSVG_1.14.0.tar.gz |
| Windows Binary (x86_64) | nnSVG_1.14.0.zip |
| macOS Binary (x86_64) | nnSVG_1.14.0.tgz |
| macOS Binary (arm64) | nnSVG_1.14.0.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 |