spoon

This is the released version of spoon; for the devel version, see spoon.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19

Address the Mean-variance Relationship in Spatial Transcriptomics Data

Bioconductor version: Release (3.23)

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

Maintainer: Kinnary Shah <kinnaryshahh at gmail.com>

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

Kinnary Shah, Boyi Guo, Stephanie C. Hicks. spoon: Address the Mean-variance Relationship in Spatial Transcriptomics Data. doi:10.18129/B9.bioc.spoon, R package version 1.8.0, https://bioconductor.org/packages/spoon.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.8.0
In Bioconductor since	BioC 3.19 (R-4.4) (2.5 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	spoon_1.8.0.tar.gz
Windows Binary (x86_64)	spoon_1.8.0.zip
macOS Binary (big-sur-x86_64)	spoon_1.8.0.tgz
macOS Binary (sonoma-arm64)	spoon_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/spoon
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/spoon
Package Short Url	https://bioconductor.org/packages/spoon/
Package Downloads Report	Download Stats