Package: SpotSweeper 1.3.3

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 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_1.3.3.tar.gz
SpotSweeper_1.3.3.zip(r-4.5)SpotSweeper_1.3.3.zip(r-4.4)
SpotSweeper_1.3.3.tgz(r-4.5-any)SpotSweeper_1.3.3.tgz(r-4.4-any)
SpotSweeper_1.3.3.tar.gz(r-4.5-noble)SpotSweeper_1.3.3.tar.gz(r-4.4-noble)
SpotSweeper_1.3.3.tgz(r-4.4-emscripten)
SpotSweeper.pdf |SpotSweeper.html
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-1.3.3(bioc 3.21)SpotSweeper-1.2.0(bioc 3.20)

softwarespatialtranscriptomicsqualitycontrolgeneexpressionbioconductorquality-controlspatial-transcriptomics

6.66 score 5 stars 77 scripts 178 downloads 6 exports 99 dependencies

Last updated 3 months agofrom:d39575fee1. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 25 2025
R-4.5-winNOTEMar 25 2025
R-4.5-macNOTEMar 25 2025
R-4.5-linuxNOTEMar 25 2025
R-4.4-winNOTEMar 25 2025
R-4.4-macNOTEMar 25 2025
R-4.4-linuxNOTEMar 25 2025

Exports:findArtifactsflagVisiumOutlierslocalOutlierslocalVarianceplotQCmetricsplotQCpdf

Dependencies:abindaskpassassortheadBHBiobaseBiocFileCacheBiocGenericsBiocNeighborsBiocParallelbitbit64blobcachemclassclassIntclicodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArraydplyre1071escheRfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrproxypurrrR6RColorBrewerRcpprjsonrlangRSQLites2S4ArraysS4VectorsscalessfSingleCellExperimentsnowSparseArrayspatialEcoSpatialExperimentstringistringrSummarizedExperimentsysterratibbletidyrtidyselectUCSC.utilsunitsutf8vctrsviridisLitewithrwkXVector

Getting started with 'SpotSweeper'

Rendered fromgetting_started.Rmdusingknitr::rmarkdownon Mar 25 2025.

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