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SpotSweeper
This is thedevelopment version of SpotSweeper; for the stable release version, seeSpotSweeper.
Spatially-aware quality control for spatial transcriptomics
Bioconductor version: Development (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]
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("SpotSweeper")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("SpotSweeper")For older versions of R, please refer to the appropriateBioconductor 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 | 1.7.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1.5 years) |
| License | MIT + fileLICENSE |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | SpotSweeper_1.7.0.tar.gz |
| Windows Binary (x86_64) | SpotSweeper_1.7.0.zip |
| macOS Binary (x86_64) | SpotSweeper_1.7.0.tgz |
| macOS Binary (arm64) | SpotSweeper_1.7.0.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 |