Package: SpatialArtifacts 1.0.0
Harriet Jiali He
SpatialArtifacts: Identification and Classification of Spatial Artifacts in Visium and Visium HD Data
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.
Authors:
SpatialArtifacts_1.0.0.tar.gz
SpatialArtifacts_1.0.0.zip(r-4.7)SpatialArtifacts_1.0.0.zip(r-4.6)SpatialArtifacts_1.0.0.zip(r-4.5)
SpatialArtifacts_1.0.0.tgz(r-4.6-any)SpatialArtifacts_1.0.0.tgz(r-4.5-any)
SpatialArtifacts_1.0.0.tar.gz(r-4.7-any)SpatialArtifacts_1.0.0.tar.gz(r-4.6-any)
SpatialArtifacts_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SpatialArtifacts/json (API)
NEWS
| # Install 'SpatialArtifacts' in R: |
| install.packages('SpatialArtifacts', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cambridgecat13/spatialartifacts/issues
- spe_vignette - Example SpatialExperiment for Vignettes
On BioConductor:SpatialArtifacts-1.1.0(bioc 3.24)SpatialArtifacts-1.0.0(bioc 3.23)
softwarespatialtranscriptomicsqualitycontroldataimportworkflowstepclassification
Last updated from:df87fa085a (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 195 | ||
| linux-devel-x86_64 | OK | 477 | ||
| source / vignettes | OK | 345 | ||
| linux-release-x86_64 | OK | 429 | ||
| macos-release-arm64 | OK | 245 | ||
| macos-oldrel-arm64 | OK | 252 | ||
| windows-devel | OK | 339 | ||
| windows-release | OK | 372 | ||
| windows-oldrel | OK | 358 | ||
| wasm-release | OK | 165 |
Exports:classifyEdgeArtifactsclumpEdgesdetectEdgeArtifactsdetectEdgeArtifacts_VisiumdetectEdgeArtifacts_VisiumHDfocal_transformationsfocal_transformations_terraproblemAreasproblemAreas_WithMorphology_terra
Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemclicodetoolscpp11curlDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2IRangeslambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6rappdirsRcpprjsonrlangRSQLiteS4ArraysS4VectorsscuttleSeqinfoSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsysterratibbletidyrtidyselectutf8vctrswithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SpatialArtifacts: Detect and Classify Spatial Artifacts | SpatialArtifacts-package SpatialArtifacts |
| Classify Edge Artifacts into Hierarchical Categories | classifyEdgeArtifacts |
| Detect edge dryspots using spatial clustering | clumpEdges |
| Unified Edge Artifact Detection | detectEdgeArtifacts |
| Detect edge artifacts in spatial transcriptomics data | detectEdgeArtifacts_Visium |
| Detect Edge Artifacts in VisiumHD Data | detectEdgeArtifacts_VisiumHD |
| Apply morphological transformations to identify connected outlier regions | focal_transformations |
| Morphological transformations using terra (optimized for VisiumHD) | focal_transformations_terra |
| Identify all problem areas in spatial transcriptomics data | problemAreas |
| Detect problem areas in VisiumHD data using morphological processing | problemAreas_WithMorphology_terra |
| Example SpatialExperiment for Vignettes | spe_vignette |
