SpotClean

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

SpotClean adjusts for spot swapping in spatial transcriptomics data

Bioconductor version: Release (3.20)

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 "4.4") and enter:


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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics
Version	1.8.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 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
System Requirements
URL	https://github.com/zijianni/SpotClean
Bug Reports	https://github.com/zijianni/SpotClean/issues

Suggests	testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	SpotClean_1.8.0.tar.gz
Windows Binary (x86_64)	SpotClean_1.8.0.zip
macOS Binary (x86_64)	SpotClean_1.8.0.tgz
macOS Binary (arm64)	SpotClean_1.8.0.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