hoodscanR

Spatial cellular neighbourhood scanning in R

Bioconductor version: Release (3.18)

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 <liu.n at wehi.edu.au>

Citation (from within R, enter citation("hoodscanR")):

Installation

To install this package, start R (version "4.3") 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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, SingleCell, Software, Spatial, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
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

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_1.0.0.tar.gz
Windows Binary	hoodscanR_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	hoodscanR_1.0.0.tgz
macOS Binary (arm64)	hoodscanR_1.0.0.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