spoon

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see spoon.

Address the Mean-variance Relationship in Spatial Transcriptomics Data

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0001-7098-2116 , Boyi Guo [aut] ORCID iD ORCID: 0000-0003-2950-2349 , Stephanie C. Hicks [aut] ORCID iD ORCID: 0000-0002-7858-0231

Maintainer: Kinnary Shah <kinnaryshahh at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("spoon")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("spoon")

spoon Tutorial HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics

Version 1.4.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

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

Suggests testthat, STexampleData, knitr, rmarkdown, BiocStyle

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package spoon_1.4.0.tar.gz

Windows Binary (x86_64) spoon_1.4.0.zip

macOS Binary (x86_64) spoon_1.4.0.tgz

macOS Binary (arm64) spoon_1.4.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/spoon

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spoon

Bioc Package Browser https://code.bioconductor.org/browse/spoon/

Package Short Url https://bioconductor.org/packages/spoon/

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