SpotSweeper
Spatially-aware quality control for spatial transcriptomics
Bioconductor version: Release (3.19)
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] 
, Stephanie Hicks [aut] , Boyi Guo [aut]
Maintainer: Michael Totty <mictott at gmail.com>
citation("SpotSweeper")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, QualityControl, Software, Spatial, Transcriptomics |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.19 (R-4.4) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices |
| System Requirements | |
| URL | https://github.com/MicTott/SpotSweeper |
| Bug Reports | https://support.bioconductor.org/tag/SpotSweeper |
See More
| 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_1.0.1.tar.gz |
| Windows Binary | SpotSweeper_1.0.0.zip |
| macOS Binary (x86_64) | SpotSweeper_1.0.1.tgz |
| macOS Binary (arm64) | SpotSweeper_1.0.1.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 |
| Old Source Packages for BioC 3.19 | Source Archive |