This is the development version of SpotSweeper; for the stable release version, see SpotSweeper.
Spatially-aware quality control for spatial transcriptomicsBioconductor version: Development (3.22)
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: 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, entercitation("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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SpotSweeper")Follow Installation instructions to use this package in your R session.
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