This is the released version of visiumStitched; for the devel version, see visiumStitched.
Enable downstream analysis of Visium capture areas stitched together with FijiBioconductor version: Release (3.21)
This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexogonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects.
Author: Nicholas J. Eagles [aut, cre] ORCID: 0000-0002-9808-5254 , Leonardo Collado-Torres [ctb] ORCID: 0000-0003-2140-308X
Maintainer: Nicholas J. Eagles <nickeagles77 at gmail.com>
Citation (from within R, entercitation("visiumStitched")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("visiumStitched")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("visiumStitched")Follow Installation instructions to use this package in your R session.
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