SpotClean
This is the development version of SpotClean; for the stable release version, see SpotClean.
SpotClean adjusts for spot swapping in spatial transcriptomics data
Bioconductor version: Development (3.21)
SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.
Author: Zijian Ni [aut, cre] (ORCID:
Maintainer: Zijian Ni <zni25 at wisc.edu>
citation("SpotClean")):
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("SpotClean")
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("SpotClean")| SpotClean | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang |
| System Requirements | |
| URL | https://github.com/zijianni/SpotClean |
| Bug Reports | https://github.com/zijianni/SpotClean/issues |
See More
| Suggests | testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling |
| 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 | SpotClean_1.9.0.tar.gz |
| Windows Binary (x86_64) | SpotClean_1.9.0.zip |
| macOS Binary (x86_64) | SpotClean_1.9.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SpotClean |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpotClean |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpotClean/ |
| Package Short Url | https://bioconductor.org/packages/SpotClean/ |
| Package Downloads Report | Download Stats |