SpotSweeper

Spatially-aware quality control for spatial transcriptomics

Bioconductor version: 3.24 · Package version: 1.9.2

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.

Installation

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

BiocManager::install("SpotSweeper")

Details

Maintainer	Michael Totty <mictott@gmail.com>
Author	Michael Totty [aut, cre] (ORCID: <https://orcid.org/0000-0002-9292-8556>), Stephanie Hicks [aut] (ORCID: <https://orcid.org/0000-0002-7858-0231>), Boyi Guo [aut] (ORCID: <https://orcid.org/0000-0003-2950-2349>)
License	MIT + file LICENSE
URL	https://github.com/MicTott/SpotSweeper
Bug Reports	https://support.bioconductor.org/tag/SpotSweeper
Downloads rank	491
Source branch	devel
biocViews	GeneExpression, QualityControl, Software, Spatial, Transcriptomics

Documentation

Getting started with 'SpotSweeper'

Download

Follow the 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 (arm64)	SpotSweeper_1.9.2.tgz
macOS binary (x86_64)	SpotSweeper_1.9.2.tgz

Dependencies

Depends: R (>= 4.4.0)

Imports: SpatialExperiment, SummarizedExperiment, S4Vectors, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, grDevices, BiocParallel

Suggests: knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0), SeuratObject, Seurat