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

Spatially-aware quality control for spatial transcriptomics

Bioconductor version: Development (3.20)

Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts. Scales linearly with the number of spots and is designed to be used with 'SpatialExperiment' objects.

Author: Michael Totty [aut, cre] , Boyi Guo [aut]

Maintainer: Michael Totty <mictott at>

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


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

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

# The following initializes usage of Bioc devel


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

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biocViews GeneExpression, QualityControl, Software, Spatial, Transcriptomics
Version 1.1.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices
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Suggests knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0)
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