clustSIGNAL
This is the released version of clustSIGNAL; for the devel version, see clustSIGNAL.
All Bioconductor versions of clustSIGNAL
3.24 (devel), 3.23 (release), 3.22, 3.21
ClustSIGNAL: a spatial clustering method
Bioconductor version: 3.23 · Package version: 1.4.1
clustSIGNAL: clustering of Spatially Informed Gene expression with Neighbourhood Adapted Learning. A tool for adaptively smoothing and clustering gene expression data. clustSIGNAL uses entropy to measure heterogeneity of cell neighbourhoods and performs a weighted, adaptive smoothing, where homogeneous neighbourhoods are smoothed more and heterogeneous neighbourhoods are smoothed less. This not only overcomes data sparsity but also incorporates spatial context into the gene expression data. The resulting smoothed gene expression data is used for clustering and could be used for other downstream analyses.
Author: Pratibha Panwar [cre, aut, ctb] 
, Boyi Guo [aut], Haowen Zhao [aut], Stephanie Hicks [aut], Shila Ghazanfar [aut, ctb]
Maintainer: Pratibha Panwar <pratibhapanwar.4 at gmail.com>
Citation
From within R, enter citation("clustSIGNAL"):
Pratibha Panwar, Boyi Guo, Haowen Zhao, Stephanie Hicks, Shila Ghazanfar. clustSIGNAL: ClustSIGNAL: a spatial clustering method. doi:10.18129/B9.bioc.clustSIGNAL, R package version 1.4.1, https://bioconductor.org/packages/clustSIGNAL.
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("clustSIGNAL")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.4.1 |
| License | GPL-2 |
| URL | https://sydneybiox.github.io/clustSIGNAL/ |
| Bug Reports | https://github.com/sydneybiox/clustSIGNAL/issues |
| Last updated | 2026-09-09 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 2086 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/clustSIGNAL/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("clustSIGNAL")| ClustSIGNAL tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | clustSIGNAL_1.4.1.tar.gz |
| Windows binary (x86_64) | clustSIGNAL_1.4.1.zip |
| macOS binary (arm64) | clustSIGNAL_1.4.1.tgz |
| macOS binary (x86_64) | clustSIGNAL_1.4.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/clustSIGNAL |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/clustSIGNAL |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |
Dependencies
Depends: R (>= 4.4.0), SpatialExperiment
Imports: BiocParallel, BiocNeighbors, bluster (>= 1.16.0), scater, harmony, SingleCellExperiment, SummarizedExperiment, methods, Matrix, reshape2
Suggests: knitr, BiocStyle, testthat (>= 3.0.0), aricode, ggplot2, patchwork, dplyr, scattermore