spatialFDA
This is the development version of spatialFDA; for the stable release version, see spatialFDA.
A Tool for Spatial Multi-sample Comparisons
Bioconductor version: Development (3.24)
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]
, Samuel Gunz [aut]
, Fabian Scheipl [aut]
, Elizabeth Purdom [aut]
, Mark D. Robinson [aut, fnd]
Maintainer: Martin Emons <martin.emons at uzh.ch>
citation("spatialFDA")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 |
| Overview Functional Data Analysis of Spatial Metrics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Software, Spatial, Transcriptomics |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL (>= 3) + file LICENSE |
| 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 |
| System Requirements | |
| URL | https://github.com/mjemons/spatialFDA |
| Bug Reports | https://github.com/mjemons/spatialFDA/issues |
See More
| Suggests | stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| 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_1.5.0.tar.gz |
| Windows Binary (x86_64) | spatialFDA_1.5.0.zip |
| macOS Binary (big-sur-x86_64) | spatialFDA_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | spatialFDA_1.5.0.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 |