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SpotClean adjusts for spot swapping in spatial transcriptomics data

Bioconductor version: Release (3.19)

SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.

Author: Zijian Ni [aut, cre] , Christina Kendziorski [ctb]

Maintainer: Zijian Ni <zni25 at>

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


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:

SpotClean HTML R Script
Reference Manual PDF


biocViews DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics
Version 1.6.1
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License GPL-3
Depends R (>= 4.2.0)
Imports stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang
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Source Package SpotClean_1.6.1.tar.gz
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macOS Binary (arm64) SpotClean_1.6.1.tgz
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