SpotSweeper

Spatially-aware quality control for spatial transcriptomics


Bioconductor version: Release (3.19)

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] , Stephanie Hicks [aut] , Boyi Guo [aut]

Maintainer: Michael Totty <mictott at gmail.com>

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

Installation

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

Details

biocViews GeneExpression, QualityControl, Software, Spatial, Transcriptomics
Version 1.0.2
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4.0)
Imports SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices
System Requirements
URL https://github.com/MicTott/SpotSweeper
Bug Reports https://support.bioconductor.org/tag/SpotSweeper
See More
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_1.0.2.tar.gz
Windows Binary SpotSweeper_1.0.2.zip
macOS Binary (x86_64) SpotSweeper_1.0.2.tgz
macOS Binary (arm64) SpotSweeper_1.0.2.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive