SpotSweeper

This is the released version of SpotSweeper; for the devel version, see SpotSweeper.

Spatially-aware quality control for spatial transcriptomics

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DOI: 10.18129/B9.bioc.SpotSweeper

Bioconductor version: Release (3.22)

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.

Author: Michael Totty [aut, cre] ORCID iD ORCID: 0000-0002-9292-8556 , Stephanie Hicks [aut] ORCID iD ORCID: 0000-0002-7858-0231 , Boyi Guo [aut] ORCID iD ORCID: 0000-0003-2950-2349

Maintainer: Michael Totty <mictott at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("SpotSweeper")

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

Documentation

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

browseVignettes("SpotSweeper")

Getting Started with `SpotSweeper` HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, QualityControl, Software, Spatial, Transcriptomics

Version 1.6.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

License MIT + file LICENSE

Depends R (>= 4.4.0)

Imports SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices, BiocParallel

System Requirements

URL https://github.com/MicTott/SpotSweeper

Bug Reports https://support.bioconductor.org/tag/SpotSweeper

Suggests knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0)

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SpotSweeper_1.6.0.tar.gz

Windows Binary (x86_64) SpotSweeper_1.6.0.zip

macOS Binary (x86_64) SpotSweeper_1.6.0.tgz

macOS Binary (arm64) SpotSweeper_1.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/SpotSweeper

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpotSweeper

Bioc Package Browser https://code.bioconductor.org/browse/SpotSweeper/

Package Short Url https://bioconductor.org/packages/SpotSweeper/

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