clustSIGNAL
ClustSIGNAL: a spatial clustering method
Bioconductor version: 3.23 · Package version: 1.4.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clustSIGNAL")Details
| Maintainer | Pratibha Panwar <pratibhapanwar.4@gmail.com> |
| Author | Pratibha Panwar [cre, aut, ctb] (ORCID: <https://orcid.org/0000-0002-7437-7084>), Boyi Guo [aut], Haowen Zhao [aut], Stephanie Hicks [aut], Shila Ghazanfar [aut, ctb] (ORCID: <https://orcid.org/0000-0001-7861-6997>) |
| License | GPL-2 |
| URL | https://sydneybiox.github.io/clustSIGNAL/ |
| Bug Reports | https://github.com/sydneybiox/clustSIGNAL/issues |
| 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/ |
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.
Documentation
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 |
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