This is the development version of spoon; for the stable release version, see spoon.

Address the Mean-variance Relationship in Spatial Transcriptomics Data

Bioconductor version: Development (3.20)

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.

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

Maintainer: Kinnary Shah <kinnaryshahh at gmail.com>

Citation (from within R, enter citation("spoon")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics
Version 1.1.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4)
Imports SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix, methods, SummarizedExperiment, stats, utils, scuttle
System Requirements
URL https://github.com/kinnaryshah/spoon
Bug Reports https://github.com/kinnaryshah/spoon/issues
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Suggests testthat, STexampleData, knitr
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Package Short Url https://bioconductor.org/packages/spoon/
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