smoothclust
This is the released version of smoothclust; for the devel version, see smoothclust.
All Bioconductor versions of smoothclust
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19
smoothclust
Bioconductor version: 3.23 · Package version: 1.8.1
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.
Author: Lukas M. Weber [aut, cre] 
Maintainer: Lukas M. Weber <weberlm3 at gmail.com>
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.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("smoothclust")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.8.1 |
| License | MIT + file LICENSE |
| URL | https://github.com/lmweber/smoothclust |
| Bug Reports | https://github.com/lmweber/smoothclust/issues |
| Last updated | 2026-07-14 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2 years) |
| Downloads rank | 2111 of 2,418 |
| 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/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("smoothclust")| Smoothclust Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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 |
| Source Repository | git clone https://git.bioconductor.org/packages/smoothclust |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/smoothclust |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |
Dependencies
Depends: R (>= 4.4.0)
Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, Matrix, methods, utils
Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat