smoothclust
smoothclust
Bioconductor version: 3.23 · Package version: 1.8.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Method for identification of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("smoothclust")Details
| Maintainer | Lukas M. Weber <weberlm3@gmail.com> |
| Author | Lukas M. Weber [aut, cre] (ORCID: <https://orcid.org/0000-0002-3282-1730>) |
| License | MIT + file LICENSE |
| URL | https://github.com/lmweber/smoothclust |
| Bug Reports | https://github.com/lmweber/smoothclust/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, GeneExpression, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/smoothclust/ |
Citation
From within R, enter citation("smoothclust"):
Lukas M. Weber. smoothclust: smoothclust. doi:10.18129/B9.bioc.smoothclust, R package version 1.8.1, https://bioconductor.org/packages/smoothclust.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | smoothclust_1.8.1.tar.gz |
| Windows binary (x86_64) | smoothclust_1.8.1.zip |
| macOS binary (arm64) | smoothclust_1.8.1.tgz |
| macOS binary (x86_64) | smoothclust_1.8.1.tgz |
Dependencies
Depends: R (>= 4.4.0)
Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, Matrix, methods, utils
Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat