spoon

Address the Mean-variance Relationship in Spatial Transcriptomics Data


Bioconductor version: Release (3.19)

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")):

Installation

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

Details

biocViews GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics
Version 1.0.0
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 Archives

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

Source Package spoon_1.0.0.tar.gz
Windows Binary spoon_1.0.0.zip (64-bit only)
macOS Binary (x86_64) spoon_1.0.0.tgz
macOS Binary (arm64) spoon_1.0.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive