Introduction | Installation | Spot-level local outlier detection | Loading example data | Calculating QC metrics using scuttle | Identifying local outliers using SpotSweeper | Visualizing local outliers | Removing technical artifacts using SpotSweeper | Visualizing technical artifacts | Identifying artifacts using SpotSweeper | Visualizing artifacts | Session information
Package: SpotSweeper 1.9.0
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 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.
Authors:
SpotSweeper_1.9.0.tar.gz
SpotSweeper_1.9.0.zip(r-4.7)SpotSweeper_1.9.0.zip(r-4.6)SpotSweeper_1.9.0.zip(r-4.5)
SpotSweeper_1.9.0.tgz(r-4.6-any)SpotSweeper_1.9.0.tgz(r-4.5-any)
SpotSweeper_1.9.0.tar.gz(r-4.7-any)SpotSweeper_1.9.0.tar.gz(r-4.6-any)
SpotSweeper_1.9.0.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-1.9.0(bioc 3.24)SpotSweeper-1.8.0(bioc 3.23)
softwarespatialtranscriptomicsqualitycontrolgeneexpressionbioconductorquality-controlspatial-transcriptomics
Last updated from:5c89af8529. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 289 | ||
| linux-devel-x86_64 | NOTE | 550 | ||
| source / vignettes | OK | 384 | ||
| linux-release-x86_64 | NOTE | 541 | ||
| macos-release-arm64 | NOTE | 441 | ||
| macos-oldrel-arm64 | NOTE | 398 | ||
| windows-devel | NOTE | 615 | ||
| windows-release | NOTE | 548 | ||
| windows-oldrel | NOTE | 580 | ||
| wasm-release | OK | 229 |
Exports:findArtifactsflagVisiumOutlierslocalOutlierslocalVarianceplotQCmetricsplotQCpdf
Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelbitbit64blobcachemclassclassIntclicodetoolscpp11curlDBIdbplyrDelayedArraydplyre1071escheRfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehttr2IRangesisobandKernSmoothlabelinglambda.rlatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigproxypurrrR6rappdirsRColorBrewerRcpprjsonrlangRSQLites2S4ArraysS4VectorsS7scalesSeqinfosfSingleCellExperimentsnowSparseArrayspatialEcoSpatialExperimentstringistringrSummarizedExperimentsysterratibbletidyrtidyselectunitsutf8vctrsviridisLitewithrwkXVector
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 Visium Outliers in SpatialExperiment Objects | flagVisiumOutliers |
| localOutliers Function | localOutliers |
| localVariance Function | localVariance |
| Plot QC metrics for a Single Sample in a SpatialExperiment object | plotQCmetrics |
| Plot Outlier Metrics to PDF | plotQCpdf |
