Package: SpotClean 1.15.0

Zijian Ni

SpotClean: SpotClean adjusts for spot swapping in spatial transcriptomics data

SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.

Authors:Zijian Ni [aut, cre], Christina Kendziorski [ctb]

SpotClean_1.15.0.tar.gz
SpotClean_1.15.0.zip(r-4.7)SpotClean_1.15.0.zip(r-4.6)SpotClean_1.15.0.zip(r-4.5)
SpotClean_1.15.0.tgz(r-4.6-any)SpotClean_1.15.0.tgz(r-4.5-any)
SpotClean_1.15.0.tar.gz(r-4.7-any)SpotClean_1.15.0.tar.gz(r-4.6-any)
SpotClean_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SpotClean/json (API)
NEWS

# Install 'SpotClean' in R:
install.packages('SpotClean', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zijianni/spotclean/issues

Datasets:
  • mbrain_raw - Example 10x Visium spatial data: raw count matrix

On BioConductor:SpotClean-1.15.0(bioc 3.24)SpotClean-1.14.0(bioc 3.23)

dataimportrnaseqsequencinggeneexpressionspatialsinglecelltranscriptomicspreprocessingrna-seqspatial-transcriptomics

6.63 score 37 stars 38 scripts 413 downloads 11 exports 177 dependencies

Last updated from:e4d13d631f. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE238
linux-devel-x86_64OK494
source / vignettesOK354
linux-release-x86_64OK552
macos-release-arm64OK448
macos-oldrel-arm64OK360
windows-develOK579
windows-releaseOK564
windows-oldrelOK499
wasm-releaseOK191

Exports:arcScoreconvertToSeuratcreateSlidekeepHighGeneread10xRawread10xRawH5read10xSlidespotcleanvisualizeHeatmapvisualizeLabelvisualizeSlide

Dependencies:abindaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsbiocmakebitbit64bitopsblobbmpbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdir.expirydotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttrhttr2icaigraphIRangesirlbaisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreadbitmapreshape2reticulaterhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownROCRrprojrootRSpectraRSQLiteRtsneS4ArraysS4VectorsS7sassscalesscattermoresctransformSeqinfoSeuratSeuratObjectshinySingleCellExperimentsitmosourcetoolsspspamSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttifftinytexutf8uwotvctrsviridisviridisLitewithrxfunxtableXVectoryamlzoo

SpotClean adjusts for spot swapping in spatial transcriptomics data

Zijian Ni and Christina Kendziorski

Rendered fromSpotClean.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-04-10
Started: 2021-05-12

Readme and manuals

Help Manual

Help pageTopics
SpotClean: a computational method to adjust for spot swapping in spatial transcriptomics dataSpotClean-package SpotClean
Calculate the ambient RNA contamination (ARC) scorearcScore arcScore.default arcScore.SummarizedExperiment
Convert slide object to Seurat objectconvertToSeurat
Create a new slide objectcreateSlide
Filter and return highly expressed or highly variable geneskeepHighGene
Example 10x Visium spatial data: raw count matrixmbrain_raw
Read 10x Space Ranger output dataread10xRaw read10xRawH5 read10xSlide
Decontaminate spot swapping effect in spatial transcriptomics dataspotclean spotclean.SpatialExperiment spotclean.SummarizedExperiment
Visualize spot values on the 2D slidevisualizeHeatmap visualizeHeatmap.default visualizeHeatmap.SummarizedExperiment
Visualize spot labels on the 2D slidevisualizeLabel visualizeLabel.default visualizeLabel.SummarizedExperiment
Visualize the Visium slide imagevisualizeSlide