clustSIGNAL
This is the released version of clustSIGNAL; for the devel version, see clustSIGNAL.
ClustSIGNAL: a spatial clustering method
Bioconductor version: Release (3.23)
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("clustSIGNAL")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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.
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 |
Details
| biocViews | Clustering, GeneExpression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.4.0), SpatialExperiment |
| Imports | BiocParallel, BiocNeighbors, bluster(>= 1.16.0), scater, harmony, SingleCellExperiment, SummarizedExperiment, methods, Matrix, reshape2 |
| System Requirements | |
| URL | https://sydneybiox.github.io/clustSIGNAL/ |
| Bug Reports | https://github.com/sydneybiox/clustSIGNAL/issues |
See More
| Suggests | knitr, BiocStyle, testthat (>= 3.0.0), aricode, ggplot2, patchwork, dplyr, scattermore |
| 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 | clustSIGNAL_1.4.0.tar.gz |
| Windows Binary (x86_64) | clustSIGNAL_1.4.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | clustSIGNAL_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | clustSIGNAL_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/clustSIGNAL |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/clustSIGNAL |
| Bioc Package Browser | https://code.bioconductor.org/browse/clustSIGNAL/ |
| Package Short Url | https://bioconductor.org/packages/clustSIGNAL/ |
| Package Downloads Report | Download Stats |