smoothclust

This is the development version of smoothclust; for the stable release version, see smoothclust.

smoothclust

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DOI: 10.18129/B9.bioc.smoothclust

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0000-0002-3282-1730

Maintainer: Lukas M. Weber <lmweb012 at gmail.com>

Citation (from within R, enter citation("smoothclust")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("smoothclust")

For older versions of R, please refer to the appropriate Bioconductor release.