SpatialFeatureExperiment
This is the development version of SpatialFeatureExperiment; for the stable release version, see SpatialFeatureExperiment.
Integrating SpatialExperiment with Simple Features in sf
Bioconductor version: Development (3.21)
A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.
Author: Lambda Moses [aut, cre] (ORCID:
Maintainer: Lambda Moses <dl3764 at columbia.edu>
citation("SpatialFeatureExperiment")):
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("SpatialFeatureExperiment")
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("SpatialFeatureExperiment")| Introduction to the SpatialFeatureExperiment class | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, Software, Spatial, Transcriptomics |
| Version | 1.9.5 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0) |
| Imports | Biobase, BiocGenerics, BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spatialreg, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot |
| System Requirements | |
| URL | https://github.com/pachterlab/SpatialFeatureExperiment |
| Bug Reports | https://github.com/pachterlab/SpatialFeatureExperiment/issues |
See More
| Suggests | arrow, BiocStyle, dplyr, knitr, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData(>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, Voyager(>= 1.7.2), withr, xml2 |
| Linking To | |
| Enhances | |
| Depends On Me | Voyager |
| Imports Me | TENxXeniumData |
| Suggests Me | concordexR, xenLite, SFEData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpatialFeatureExperiment_1.9.5.tar.gz |
| Windows Binary (x86_64) | SpatialFeatureExperiment_1.9.5.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | SpatialFeatureExperiment_1.9.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpatialFeatureExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpatialFeatureExperiment |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpatialFeatureExperiment/ |
| Package Short Url | https://bioconductor.org/packages/SpatialFeatureExperiment/ |
| Package Downloads Report | Download Stats |