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This is the development version of hoodscanR; for the stable release version, see hoodscanR.

Spatial cellular neighbourhood scanning in R

Bioconductor version: Development (3.20)

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))

# The following initializes usage of Bioc devel


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 1.3.0
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)
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Suggests testthat (>= 3.0.0), BiocStyle
Linking To Rcpp
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Follow Installation instructions to use this package in your R session.

Source Package hoodscanR_1.3.0.tar.gz
Windows Binary
macOS Binary (x86_64) hoodscanR_1.3.0.tgz
macOS Binary (arm64) hoodscanR_1.3.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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