roramirezf / SpatialExperiment

SpatialExperiment

SpatialExperiment package provides an S4 class for Spatial Omics data handling.

Since version 1.1.42 SpatialExperiment package has changed in several ways.

• VisiumExperiment and SpatialExperiment classes are merged into the SpatialExperiment class.
• Newer version of SpatialExperiment has image loading handling with imgData structure
• Molecular-based data can be handled with molecular BumpyMatrix assay.
• 10x Visium standard data import support with read10xVisium function.
• Check vignettes and documentation for further details.

Installation

SpatialExperiment is available on the Bioductor official repository. Today (January 2021) version 1.1.42 is available on Bioconductor devel (v3.13).

To install it use:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SpatialExperiment")

or, alternatively, use the following for the latest github-devel version:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("drighelli/SpatialExperiment")

Add-ons

Spatial Experiment and multimodal data

SpatialExperiment class can be included into a MultiAssayExperiment object as a dedicated assay. Check how it handles seqFISH data into the SingleCellMultiModal::seqFISH() package function.

SingleCellMultiModal is available in Bioconductor and can be installed via:

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

BiocManager::install("SingleCellMultiModal")

Spatial Analysis

To provide additional examples for spatial transcriptomics analysis we're constantly populating the https://github.com/drighelli/SpatialAnalysisWorkflows repository.

These will hopefully find a place into a dedicated package for Spatial Transcriptomics data analysis examples.