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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

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
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_1.0.0.tar.gz
Windows Binary hoodscanR_1.0.0.zip
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