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.
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")
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")
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.