smoothclust
This is the development version of smoothclust; for the stable release version, see smoothclust.
smoothclust
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Lukas M. Weber <lmweberedu at gmail.com>
citation("smoothclust")):
Installation
To install this package, start R (version "4.5") 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.
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 | |
| LICENSE | Text |
Details
| biocViews | Clustering, GeneExpression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | smoothclust_1.3.0.tar.gz |
| Windows Binary (x86_64) | smoothclust_1.3.0.zip |
| macOS Binary (x86_64) | smoothclust_1.3.0.tgz |
| macOS Binary (arm64) | |
| 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 |