spatialFDA
This is the development version of spatialFDA; to use it, please install the devel version of Bioconductor.
A Tool for Spatial Multi-sample Comparisons
Bioconductor version: Development (3.21)
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.
Author: Martin Emons [aut, cre] (ORCID:
Maintainer: Martin Emons <martin.emons at uzh.ch>
citation("spatialFDA")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("spatialFDA")
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("spatialFDA")| Functional Data Analysis of Spatial Metrics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Software, Spatial, Transcriptomics |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | GPL (>= 3) + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | dplyr, ggplot2, parallel, patchwork, purrr, refund, SpatialExperiment, spatstat.explore, spatstat.geom, SummarizedExperiment, tidyr, methods, stats, fda, graphics, magrittr |
| System Requirements | |
| URL | https://github.com/mjemons/spatialFDA |
| Bug Reports | https://github.com/mjemons/spatialFDA/issues |
See More
| Suggests | imcdatasets, stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) |
| 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 | spatialFDA_0.99.7.tar.gz |
| Windows Binary (x86_64) | spatialFDA_0.99.7.zip (64-bit only) |
| macOS Binary (x86_64) | spatialFDA_0.99.7.tgz |
| macOS Binary (arm64) | spatialFDA_0.99.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/spatialFDA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spatialFDA |
| Bioc Package Browser | https://code.bioconductor.org/browse/spatialFDA/ |
| Package Short Url | https://bioconductor.org/packages/spatialFDA/ |
| Package Downloads Report | Download Stats |