Package: SpotClean 1.7.1
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:
SpotClean_1.7.1.tar.gz
SpotClean_1.7.1.zip(r-4.5)SpotClean_1.7.1.zip(r-4.4)SpotClean_1.7.1.zip(r-4.3)
SpotClean_1.7.1.tgz(r-4.4-any)SpotClean_1.7.1.tgz(r-4.3-any)
SpotClean_1.7.1.tar.gz(r-4.5-noble)SpotClean_1.7.1.tar.gz(r-4.4-noble)
SpotClean_1.7.1.tgz(r-4.4-emscripten)
SpotClean.pdf |SpotClean.html✨
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
- mbrain_raw - Example 10x Visium spatial data: raw count matrix
On BioConductor:SpotClean-1.7.1(bioc 3.20)SpotClean-1.6.1(bioc 3.19)
Last updated 1 months agofrom:27c955af90
Exports:arcScoreconvertToSeuratcreateSlidekeepHighGeneread10xRawread10xRawH5read10xSlidespotcleanvisualizeHeatmapvisualizeLabelvisualizeSlide
Dependencies:abindaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsbitbit64bitopsblobbmpbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplogrplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreadbitmapreshape2reticulaterhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownROCRrprojrootRSpectraRSQLiteRtsneS4ArraysS4VectorssassscalesscattermoresctransformSeuratSeuratObjectshinySingleCellExperimentsitmosourcetoolsspspamSparseArraySpatialExperimentspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttifftinytexUCSC.utilsutf8uwotvctrsviridisviridisLitewithrxfunxtableXVectoryamlzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SpotClean: a computational method to adjust for spot swapping in spatial transcriptomics data | SpotClean-package SpotClean |
| Calculate the ambient RNA contamination (ARC) score | arcScore arcScore.default arcScore.SummarizedExperiment |
| Convert slide object to Seurat object | convertToSeurat |
| Create a new slide object | createSlide |
| Filter and return highly expressed or highly variable genes | keepHighGene |
| Example 10x Visium spatial data: raw count matrix | mbrain_raw |
| Read 10x Space Ranger output data | read10xRaw read10xRawH5 read10xSlide |
| Decontaminate spot swapping effect in spatial transcriptomics data | spotclean spotclean.SpatialExperiment spotclean.SummarizedExperiment |
| Visualize spot values on the 2D slide | visualizeHeatmap visualizeHeatmap.default visualizeHeatmap.SummarizedExperiment |
| Visualize spot labels on the 2D slide | visualizeLabel visualizeLabel.default visualizeLabel.SummarizedExperiment |
| Visualize the Visium slide image | visualizeSlide |
