Registration Open for Bioc2024 July 24-26


Spatial cellular neighbourhood scanning in R

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

hoodscanR_introduction HTML R Script
Reference Manual PDF


biocViews Clustering, SingleCell, Software, Spatial, Transcriptomics
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 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
Bug Reports
See More
Suggests testthat (>= 3.0.0), BiocStyle
Linking To Rcpp
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_1.2.0.tar.gz
Windows Binary
macOS Binary (x86_64) hoodscanR_1.2.0.tgz
macOS Binary (arm64) hoodscanR_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats