Introduction | Assay and chemistry support | Installation | Spot-level local outlier detection | Loading example data | Calculating QC metrics using scuttle | Identifying local outliers using SpotSweeper | Using a Seurat object | Visualizing local outliers | Removing technical artifacts using SpotSweeper | Visualizing technical artifacts | Identifying artifacts using SpotSweeper | Visualizing artifacts | Session information
Package: SpotSweeper 1.9.3
Michael Totty
SpotSweeper: Spatially-aware quality control for spatial transcriptomics
Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcriptomics, 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 outlier spots and large technical artifacts.
Authors:
SpotSweeper_1.9.3.tar.gz
SpotSweeper_1.9.3.zip(r-4.7-any)SpotSweeper_1.9.3.zip(r-4.6-any)SpotSweeper_1.9.3.zip(r-4.5-any)
SpotSweeper_1.9.3.tgz(r-4.6-any)SpotSweeper_1.9.3.tgz(r-4.5-any)
SpotSweeper_1.9.3.tar.gz(r-4.7-any)SpotSweeper_1.9.3.tar.gz(r-4.6-any)
SpotSweeper_1.9.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SpotSweeper/json (API)
| # Install 'SpotSweeper' in R: |
| install.packages('SpotSweeper', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mictott/spotsweeper/issues
Datasets:
- biased_spots - Biased Spots Data
- DLPFC_artifact - Human DLPFC dataset with a technical artifact (hangnail).
On BioConductor:SpotSweeper-1.9.2(bioc 3.24)SpotSweeper-1.8.0(bioc 3.23)
softwarespatialtranscriptomicsqualitycontrolgeneexpressionbioconductorquality-controlspatial-transcriptomics
Last updated from:7e6ebf68c2. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 207 | ||
| linux-devel | OK | 487 | ||
| source / vignettes | OK | 341 | ||
| linux-release | OK | 467 | ||
| macos-release | OK | 406 | ||
| macos-oldrel | OK | 351 | ||
| windows-devel | OK | 485 | ||
| windows-release | OK | 384 | ||
| windows-oldrel | OK | 489 | ||
| wasm-release | OK | 186 |
Exports:findArtifactsflagVisiumOutliersgetMetadatagetSpatialCoordslocalOutlierslocalVarianceplotQCmetricsplotQCpdfsetMetadatasubsetSpatialObjectvalidateMetadataColumns
Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelbitbit64blobcachemclicodetoolscpp11curlDBIdbplyrDelayedArraydplyrescheRfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehttr2IRangesisobandlabelinglambda.rlatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6RColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Biased Spots Data | biased_spots |
| human DLPFC dataset with a technical artifact (hangnail). | DLPFC_artifact |
| Identify and annotate artifacts in spatial transcriptomics data | findArtifacts |
| Flag systematic Visium outlier positions | flagVisiumOutliers |
| Get column metadata from a spatial object | getMetadata |
| Get spatial coordinates from a spatial object | getSpatialCoords |
| Detect local outliers in spatial transcriptomics data | localOutliers |
| localVariance Function | localVariance |
| Plot QC metrics for a Single Sample in a SpatialExperiment object | plotQCmetrics |
| Plot Outlier Metrics to PDF | plotQCpdf |
| Replace column metadata in a spatial object | setMetadata |
| Subset a spatial object by spots | subsetSpatialObject |
| Validate columns in spatial-object metadata | validateMetadataColumns |