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smoothclust

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19

smoothclust

DOI: 10.18129/B9.bioc.smoothclust

Bioconductor version: Development (3.24)

Tools for spatial domain analysis in spatial transcriptomics data. Includes spatial smoothing of gene expression profiles for downstream clustering and a boundary density (BD) metric for summarizing spatial domain organization. The smoothing function returns processed expression values for subsequent clustering. BD requires only spatial coordinates and categorical labels, and provides local and sample-level summaries of label transitions.

Author: Lukas M. Weber [aut, cre] ORCID: 0000-0002-3282-1730

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 1.9.6, 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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

Details

Package Archives

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