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Spatial transcriptomic clustering

Bioconductor version: Release (3.19)

Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.

Author: Vipul Singhal [aut], Joseph Lee [aut, cre]

Maintainer: Joseph Lee <joseph.lee at>

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


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:

Domain segmentation (STARmap PLUS mouse brain) HTML R Script
Multi-sample analysis (10x Visium Human DLPFC) HTML R Script
Parameter selection (VeraFISH Mouse Hippocampus) HTML R Script
Spatial data integration with Harmony (10x Visium Human DLPFC) HTML R Script
Reference Manual PDF


biocViews Clustering, DimensionReduction, GeneExpression, SingleCell, Software, Spatial
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License file LICENSE
Depends R (>= 4.4.0)
Imports aricode, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, matrixStats, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian
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Suggests knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package Banksy_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64) Banksy_1.0.0.tgz
macOS Binary (arm64) Banksy_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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