hoodscanR
This is the released version of hoodscanR; for the devel version, see hoodscanR.
Spatial cellular neighbourhood scanning in R
Bioconductor version: Release (3.23)
hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.
Author: Ning Liu [aut, cre]
, Jarryd Martin [aut]
Maintainer: Ning Liu <ning.liu at adelaide.edu.au>
citation("hoodscanR")):
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("hoodscanR")
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("hoodscanR")| hoodscanR_introduction | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.3) |
| Imports | knitr, rmarkdown, SpatialExperiment, SummarizedExperiment, circlize, ComplexHeatmap, scico, rlang, utils, ggplot2, grid, methods, stats, RANN, Rcpp (>= 1.0.9) |
| System Requirements | |
| URL | https://github.com/DavisLaboratory/hoodscanR https://davislaboratory.github.io/hoodscanR/ |
| Bug Reports | https://github.com/DavisLaboratory/hoodscanR/issues |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | hoodscanR_1.10.0.tar.gz |
| Windows Binary (x86_64) | hoodscanR_1.10.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | hoodscanR_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | hoodscanR_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/hoodscanR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/hoodscanR |
| Bioc Package Browser | https://code.bioconductor.org/browse/hoodscanR/ |
| Package Short Url | https://bioconductor.org/packages/hoodscanR/ |
| Package Downloads Report | Download Stats |