Package: spoon 1.3.2

Kinnary Shah

spoon: Address the Mean-variance Relationship in Spatial Transcriptomics Data

This package addresses the mean-variance relationship in spatially resolved transcriptomics data. Precision weights are generated for individual observations using Empirical Bayes techniques. These weights are used to rescale the data and covariates, which are then used as input in spatially variable gene detection tools.

Authors:Kinnary Shah [aut, cre], Boyi Guo [aut], Stephanie C. Hicks [aut]

spoon_1.3.2.tar.gz
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spoon.pdf |spoon.html✨
spoon/json (API)
NEWS

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

Bug tracker:https://github.com/kinnaryshah/spoon/issues

On BioConductor:spoon-1.3.1(bioc 3.21)spoon-1.2.0(bioc 3.20)

spatialsinglecelltranscriptomicsgeneexpressionpreprocessing

4.88 score 19 scripts 124 downloads 2 exports 81 dependencies

Last updated 27 days agofrom:34388069ae. Checks:3 OK, 3 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 12 2025
R-4.5-winERRORFeb 12 2025
R-4.5-macERRORFeb 12 2025
R-4.5-linuxERRORFeb 12 2025
R-4.4-winOKFeb 12 2025
R-4.4-macOKFeb 12 2025

Exports:generate_weightsweighted_nnSVG

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobBRISCcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennSVGopensslpbapplypillarpkgconfigplogrpurrrR6RANNRcppRcppArmadillordistrjsonrlangRSQLiteS4ArraysS4VectorsscuttleSingleCellExperimentsnowSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVector

spoon Tutorial

Kinnary H. Shah, Boyi Guo, Stephanie C. Hicks

Rendered fromspoon.Rmdusingknitr::rmarkdownon Feb 12 2025.

Last update: 2024-11-01
Started: 2024-01-22

Readme and manuals

Help Manual

Help pageTopics
Generate weightsgenerate_weights
Weighted nnSVGweighted_nnSVG