nnSVG
This is the released version of nnSVG; for the devel version, see nnSVG.
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]
, Stephanie C. Hicks [aut]
Maintainer: Lukas M. Weber <weberlm3 at gmail.com>
citation("nnSVG")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/nnSVG/ |
| Package Short Url | https://bioconductor.org/packages/nnSVG/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |