SpotClean

DOI: 10.18129/B9.bioc.SpotClean  

SpotClean adjusts for spot swapping in spatial transcriptomics data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	SpotClean
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics
Version	1.0.1
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
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
LinkingTo
Suggests	testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling
SystemRequirements
Enhances
URL	https://github.com/zijianni/SpotClean
BugReports	https://github.com/zijianni/SpotClean/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SpotClean_1.0.1.tar.gz
Windows Binary	SpotClean_1.0.1.zip
macOS Binary (x86_64)	SpotClean_1.0.1.tgz
macOS Binary (arm64)	SpotClean_1.0.1.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
Old Source Packages for BioC 3.16	Source Archive