smoothclust

smoothclust


Bioconductor version: Release (3.19)

Method for segmentation 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 <lmweberedu at gmail.com>

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

Installation

To install this package, start R (version "4.4") 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.

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 PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, GeneExpression, SingleCell, Software, Spatial, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4.0)
Imports SpatialExperiment, SummarizedExperiment, sparseMatrixStats, spdep, methods, utils
System Requirements
URL https://github.com/lmweber/smoothclust
Bug Reports https://github.com/lmweber/smoothclust/issues
See More
Suggests BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package smoothclust_1.0.0.tar.gz
Windows Binary (x86_64) smoothclust_1.0.0.zip
macOS Binary (x86_64) smoothclust_1.0.0.tgz
macOS Binary (arm64) smoothclust_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/smoothclust
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/smoothclust
Bioc Package Browser https://code.bioconductor.org/browse/smoothclust/
Package Short Url https://bioconductor.org/packages/smoothclust/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive