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:Michael Totty [aut, cre], Stephanie Hicks [aut], Boyi Guo [aut]

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✨
card.svg |card.png
SpotSweeper/json (API)
NEWS

# 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:

On BioConductor:SpotSweeper-1.9.0(bioc 3.24)SpotSweeper-1.8.0(bioc 3.23)

softwarespatialtranscriptomicsqualitycontrolgeneexpressionbioconductorquality-controlspatial-transcriptomics

6.93 score 16 stars 179 scripts 386 downloads 6 exports 91 dependencies

Last updated from:5c89af8529. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING289
linux-devel-x86_64NOTE550
source / vignettesOK384
linux-release-x86_64NOTE541
macos-release-arm64NOTE441
macos-oldrel-arm64NOTE398
windows-develNOTE615
windows-releaseNOTE548
windows-oldrelNOTE580
wasm-releaseOK229

Exports:findArtifactsflagVisiumOutlierslocalOutlierslocalVarianceplotQCmetricsplotQCpdf

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelbitbit64blobcachemclassclassIntclicodetoolscpp11curlDBIdbplyrDelayedArraydplyre1071escheRfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehttr2IRangesisobandKernSmoothlabelinglambda.rlatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigproxypurrrR6rappdirsRColorBrewerRcpprjsonrlangRSQLites2S4ArraysS4VectorsS7scalesSeqinfosfSingleCellExperimentsnowSparseArrayspatialEcoSpatialExperimentstringistringrSummarizedExperimentsysterratibbletidyrtidyselectunitsutf8vctrsviridisLitewithrwkXVector

Getting started with 'SpotSweeper'

Michael Totty, Boyi Guo, Stephanie Hicks

Rendered fromgetting_started.Rmdusingknitr::rmarkdownon Jun 10 2026.

Last update: 2024-11-08
Started: 2024-02-13