spoon
Address the Mean-variance Relationship in Spatial Transcriptomics Data
Bioconductor version: 3.23 · Package version: 1.8.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spoon")Details
| Maintainer | Kinnary Shah <kinnaryshahh@gmail.com> |
| Author | Kinnary Shah [aut, cre] (ORCID: <https://orcid.org/0000-0001-7098-2116>), Boyi Guo [aut] (ORCID: <https://orcid.org/0000-0003-2950-2349>), Stephanie C. Hicks [aut] (ORCID: <https://orcid.org/0000-0002-7858-0231>) |
| License | MIT + file LICENSE |
| URL | https://github.com/kinnaryshah/spoon |
| Bug Reports | https://github.com/kinnaryshah/spoon/issues |
| Downloads rank | 292 |
| Source branch | RELEASE_3_23 |
| biocViews | GeneExpression, Preprocessing, SingleCell, Software, Spatial, Transcriptomics |
Documentation
Download
Follow the 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 (arm64) | spoon_1.8.0.tgz |
| macOS binary (x86_64) | spoon_1.8.0.tgz |
Dependencies
Depends: R (>= 4.4)
Imports: SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix, methods, SummarizedExperiment, stats, utils, scuttle
Suggests: testthat, STexampleData, knitr, rmarkdown, BiocStyle