README.md

SpatialFeatureExperiment

Lifecycle: experimental codecov R-CMD-check

Installation

This package is available on Bioconductor version 3.16 and above. It can be installed with

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("SpatialFeatureExperiment")

Documentation can be accessed on this website.

Introduction

SpatialFeatureExperiment (SFE) is a new S4 class built on top of SpatialExperiment (SPE). SpatialFeatureExperiment incorporates geometries and geometry operations with the sf package. Examples of supported geometries are Visium spots represented with polygons corresponding to their size, cell or nuclei segmentation polygons, tissue boundary polygons, pathologist annotation of histological regions, and transcript spots of genes. Using sf, SpatialFeatureExperiment leverages well-established and optimized C++ libraries underlying sf for geometry operations, including algorithms for determining whether geometries intersect, finding intersection geometries, buffering geometries with margins, etc. A schematic of the SFE object is shown below:

Below is a list of SFE features that extend the SPE object:

Citation

Voyager: exploratory single-cell genomics data analysis with geospatial statistics. Lambda Moses, Pétur Helgi Einarsson, Kayla Jackson, Laura Luebbert, A. Sina Booeshaghi, Sindri Antonsson, Páll Melsted, Lior Pachter bioRxiv 2023.07.20.549945; doi: https://doi.org/10.1101/2023.07.20.549945



pachterlab/SpatialFeatureExperiment documentation built on Aug. 23, 2024, 11:38 p.m.