SpotSweeper
This is the released version of SpotSweeper; for the devel version, see SpotSweeper.
Spatially-aware quality control for spatial transcriptomics
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 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 |
See More
| Suggests | knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | SpotSweeper_1.8.0.zip |
| macOS Binary (big-sur-x86_64) | SpotSweeper_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | SpotSweeper_1.8.0.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 |