SpatialArtifacts
This is the development version of SpatialArtifacts; to use it, please install the devel version of Bioconductor.
Identification and Classification of Spatial Artifacts in Visium and Visium HD Data
Bioconductor version: Development (3.23)
SpatialArtifacts provides a data-driven two-step workflow to identify, classify, and handle spatial artifacts in spatial transcriptomics data. The package combines median absolute deviation (MAD)-based outlier detection with morphological image processing (fill, outline, and star patterns) to detect edge and interior artifacts. It supports multiple platforms including 10x Genomics Visium (standard and HD), allowing for consistent quality control across different spatial resolutions.
Author: Harriet Jiali He [aut, cre]
, Jacqueline R. Thompson [aut], Michael Totty [aut], Stephanie C. Hicks [aut, fnd]
Maintainer: Harriet Jiali He <jhe46 at jh.edu>
citation("SpatialArtifacts")):
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 devel
BiocManager::install(version='devel')
BiocManager::install("SpatialArtifacts")
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("SpatialArtifacts")| SpatialArtifacts Tutorial | HTML | R Script |
| Reference Manual |
Details
| biocViews | Classification, DataImport, QualityControl, Software, Spatial, Transcriptomics, WorkflowStep |
| Version | 0.99.8 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.6.0) |
| Imports | SpatialExperiment, SummarizedExperiment, S4Vectors, scuttle, dplyr, terra, stats, methods |
| System Requirements | quarto, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0) |
| URL | https://github.com/CambridgeCat13/SpatialArtifacts |
| Bug Reports | https://github.com/CambridgeCat13/SpatialArtifacts/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, BiocCheck, ggplot2, patchwork, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpatialArtifacts_0.99.8.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | SpatialArtifacts_0.99.8.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpatialArtifacts |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpatialArtifacts |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpatialArtifacts/ |
| Package Short Url | https://bioconductor.org/packages/SpatialArtifacts/ |
| Package Downloads Report | Download Stats |