spatialFDA
A Tool for Spatial Multi-sample Comparisons
Bioconductor version: 3.24 · Package version: 1.5.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
spatialFDA is a package to calculate spatial statistics metrics. The package takes a SpatialExperiment object and calculates spatial statistics metrics using the package spatstat. Then it compares the resulting functions across samples/conditions using functional additive models as implemented in the package refund. Furthermore, it provides exploratory visualisations using functional principal component analysis, as well implemented in refund.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spatialFDA")Details
| Maintainer | Martin Emons <martin.emons@uzh.ch> |
| Author | Martin Emons [aut, cre] (ORCID: <https://orcid.org/0009-0000-5219-5311>), Samuel Gunz [aut] (ORCID: <https://orcid.org/0000-0002-8909-0932>), Fabian Scheipl [aut] (ORCID: <https://orcid.org/0000-0001-8172-3603>), Elizabeth Purdom [aut] (ORCID: <https://orcid.org/0000-0001-9455-7990>), Mark D. Robinson [aut, fnd] (ORCID: <https://orcid.org/0000-0002-3048-5518>) |
| License | GPL (>= 3) + file LICENSE |
| URL | https://github.com/mjemons/spatialFDA |
| Bug Reports | https://github.com/mjemons/spatialFDA/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/spatialFDA/ |
Citation
From within R, enter citation("spatialFDA"):
Martin Emons, Samuel Gunz, Fabian Scheipl, Elizabeth Purdom, Mark D. Robinson. spatialFDA: A Tool for Spatial Multi-sample Comparisons. doi:10.18129/B9.bioc.spatialFDA, R package version 1.5.2, https://bioconductor.org/packages/spatialFDA.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | spatialFDA_1.5.2.tar.gz |
| Windows binary (x86_64) | spatialFDA_1.5.2.zip |
| macOS binary (arm64) | spatialFDA_1.5.2.tgz |
| macOS binary (x86_64) | spatialFDA_1.5.2.tgz |
Dependencies
Depends: R (>= 4.3.0)
Imports: dplyr, ggplot2, parallel, patchwork, purrr, refund, SpatialExperiment, spatstat.explore, spatstat.geom, SummarizedExperiment, methods, stats, fda, tidyr, graphics, ExperimentHub, scales, S4Vectors, mgcv
Suggests: stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)