SpotSweeper

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19

Spatially-aware quality control for spatial transcriptomics

Bioconductor version: Development (3.24)

Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcriptomics, 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 outlier spots and large technical artifacts.

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

Maintainer: Michael Totty <mictott at gmail.com>

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

Michael Totty, Stephanie Hicks, Boyi Guo. SpotSweeper: Spatially-aware quality control for spatial transcriptomics. doi:10.18129/B9.bioc.SpotSweeper, R package version 1.9.2, https://bioconductor.org/packages/SpotSweeper.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.9.2
In Bioconductor since	BioC 3.19 (R-4.4) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.4.0)
Imports	SpatialExperiment, SummarizedExperiment, S4Vectors, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, 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), SeuratObject, Seurat
Linking To
Enhances
Depends On Me
Imports Me	OSTA
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SpotSweeper_1.9.2.tar.gz
Windows Binary (x86_64)	SpotSweeper_1.9.2.zip
macOS Binary (big-sur-x86_64)	SpotSweeper_1.9.2.tgz
macOS Binary (sonoma-arm64)	SpotSweeper_1.9.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpotSweeper
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpotSweeper
Package Short Url	https://bioconductor.org/packages/SpotSweeper/
Package Downloads Report	Download Stats