spoon
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see spoon.
Address the Mean-variance Relationship in Spatial Transcriptomics Data
Bioconductor version: 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("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 | ||
| 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 |
See More
| Suggests | testthat, STexampleData, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spoon_1.0.0.tar.gz |
| Windows Binary (x86_64) | 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 |