SpatialArtifacts
Identification and Classification of Spatial Artifacts in Visium and Visium HD Data
Bioconductor version: 3.24 · Package version: 1.1.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpatialArtifacts")Details
| Maintainer | Harriet Jiali He <jhe46@jh.edu> |
| Author | Harriet Jiali He [aut, cre] (ORCID: <https://orcid.org/0009-0003-7827-2735>), Jacqueline R. Thompson [aut], Michael Totty [aut], Stephanie C. Hicks [aut, fnd] (ORCID: <https://orcid.org/0000-0002-7858-0231>) |
| License | Artistic-2.0 |
| URL | https://github.com/CambridgeCat13/SpatialArtifacts |
| Bug Reports | https://github.com/CambridgeCat13/SpatialArtifacts/issues |
| System Requirements | quarto, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, DataImport, QualityControl, Software, Spatial, Transcriptomics, WorkflowStep |
| Package Short Url | https://bioconductor.org/packages/SpatialArtifacts/ |
Citation
From within R, enter citation("SpatialArtifacts"):
Harriet Jiali He, Jacqueline R. Thompson, Michael Totty, Stephanie C. Hicks. SpatialArtifacts: Identification and Classification of Spatial Artifacts in Visium and Visium HD Data. doi:10.18129/B9.bioc.SpatialArtifacts, R package version 1.1.0, https://bioconductor.org/packages/SpatialArtifacts.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SpatialArtifacts_1.1.0.tar.gz |
| Windows binary (x86_64) | SpatialArtifacts_1.1.0.zip |
| macOS binary (arm64) | SpatialArtifacts_1.1.0.tgz |
| macOS binary (x86_64) | SpatialArtifacts_1.1.0.tgz |
Dependencies
Depends: R (>= 4.4.0)
Imports: SpatialExperiment, SummarizedExperiment, S4Vectors, scuttle, dplyr, terra, stats, methods
Suggests: BiocStyle, knitr, rmarkdown, BiocCheck, ggplot2, patchwork, testthat (>= 3.0.0)