Package: SpotSweeper 1.3.0

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. Scales linearly with the number of spots and is designed to be used with 'SpatialExperiment' objects.

Authors:Michael Totty [aut, cre], Boyi Guo [aut]

SpotSweeper_1.3.0.tar.gz
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SpotSweeper_1.3.0.tgz(r-4.4-any)SpotSweeper_1.3.0.tgz(r-4.3-any)
SpotSweeper_1.3.0.tar.gz(r-4.5-noble)SpotSweeper_1.3.0.tar.gz(r-4.4-noble)
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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'))

Peer review:

Bug tracker:https://github.com/mictott/spotsweeper/issues

Datasets:
  • DLPFC_artifact - Human DLPFC dataset with a technical artifact (hangnail).

On BioConductor:SpotSweeper-1.3.0(bioc 3.21)SpotSweeper-1.1.0(bioc 3.20)

softwarespatialtranscriptomicsqualitycontrolgeneexpressionbioconductorquality-controlspatial-transcriptomics

6.46 score 3 stars 53 scripts 173 downloads 5 exports 92 dependencies

Last updated 22 days agofrom:49fbeaa64b. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winERROROct 31 2024
R-4.5-linuxERROROct 31 2024
R-4.4-winERROROct 31 2024
R-4.4-macERROROct 31 2024
R-4.3-winERROROct 31 2024
R-4.3-macERROROct 31 2024

Exports:findArtifactslocalOutlierslocalVarianceplotQCplotQCpdf

Dependencies:abindaskpassassortheadBiobaseBiocFileCacheBiocGenericsBiocNeighborsbitbit64blobcachemclassclassIntclicolorspacecpp11crayoncurlDBIdbplyrDelayedArraydplyre1071escheRfansifarverfastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKernSmoothlabelinglatticelifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrproxypurrrR6RColorBrewerRcpprjsonrlangRSQLites2S4ArraysS4VectorsscalessfSingleCellExperimentSparseArrayspatialEcoSpatialExperimentstringistringrSummarizedExperimentsysterratibbletidyrtidyselectUCSC.utilsunitsutf8vctrsviridisLitewithrwkXVectorzlibbioc

Getting started with 'SpotSweeper'

Michael Totty, Boyi Guo, Stephanie Hicks

Rendered fromgetting_started.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-04-10
Started: 2024-02-13