hoodscanR
This is the development version of hoodscanR; for the stable release version, see hoodscanR.
Spatial cellular neighbourhood scanning in R
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Ning Liu <liu.n at wehi.edu.au>
citation("hoodscanR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.5.1 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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 | |
| 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_1.5.1.tar.gz |
| Windows Binary (x86_64) | hoodscanR_1.5.1.zip (64-bit only) |
| macOS Binary (x86_64) | hoodscanR_1.5.1.tgz |
| macOS Binary (arm64) | hoodscanR_1.5.1.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 |