smoothclust
This is the development version of smoothclust; for the stable release version, see smoothclust.
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]
Maintainer: Lukas M. Weber <weberlm3 at gmail.com>
citation("smoothclust")):
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")
## 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")| Smoothclust Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GeneExpression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.9.6 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | SpatialExperiment, SummarizedExperiment, S4Vectors, BiocNeighbors, Matrix, methods, utils |
| System Requirements | |
| URL | https://github.com/lmweber/smoothclust |
| Bug Reports | https://github.com/lmweber/smoothclust/issues |
See More
| Suggests | BiocStyle, knitr, STexampleData, 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_1.9.6.tar.gz |
| Windows Binary (x86_64) | smoothclust_1.9.6.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | smoothclust_1.9.6.tgz |
| macOS Binary (sonoma-arm64) | smoothclust_1.9.6.tgz |
| 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 |