SpotSweeper

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

Spatially-aware quality control for spatial transcriptomics

Bioconductor version: Development (3.21)

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] (ORCID: ), Stephanie Hicks [aut] (ORCID: ), Boyi Guo [aut] (ORCID: )

Maintainer: Michael Totty <mictott at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
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	1.3.3
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.4.0)
Imports	SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, 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)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	SpotSweeper_1.3.3.tar.gz
Windows Binary (x86_64)	SpotSweeper_1.3.3.zip
macOS Binary (x86_64)	SpotSweeper_1.3.3.tgz
macOS Binary (arm64)	SpotSweeper_1.3.3.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