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SpotClean

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

SpotClean adjusts for spot swapping in spatial transcriptomics data

Bioconductor version: Development (3.18)

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 wisc.edu>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SpotClean")

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("SpotClean")
SpotClean HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics
Version 1.3.0
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
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
Linking To
Suggests testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling
System Requirements
Enhances
URL https://github.com/zijianni/SpotClean
Bug Reports https://github.com/zijianni/SpotClean/issues
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Package Archives

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

Source Package SpotClean_1.3.0.tar.gz
Windows Binary SpotClean_1.3.0.zip
macOS Binary (x86_64) SpotClean_1.3.0.tgz
macOS Binary (arm64) SpotClean_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SpotClean
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpotClean
Bioc Package Browser https://code.bioconductor.org/browse/SpotClean/
Package Short Url https://bioconductor.org/packages/SpotClean/
Package Downloads Report Download Stats