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Bioconductor - visiumStitched (development version)

visiumStitched

This is the development version of visiumStitched; for the stable release version, see visiumStitched.

Enable downstream analysis of Visium capture areas stitched together with Fiji

Bioconductor version: Development (3.22)

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, enter citation("visiumStitched")): 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("visiumStitched")

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("visiumStitched")
Details biocViews DataImport, GeneExpression, Software, Spatial, Transcription, Transcriptomics, Visualization Version 1.1.0 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) License Artistic-2.0 Depends R (>= 4.4), SpatialExperiment Imports BiocBaseUtils, BiocGenerics, dplyr, DropletUtils, grDevices, imager, Matrix, methods, pkgcond, readr, rjson, S4Vectors, SingleCellExperiment, spatialLIBD(>= 1.17.8), stringr, SummarizedExperiment, tibble, tidyr, xml2 System Requirements URL https://github.com/LieberInstitute/visiumStitched Bug Reports https://support.bioconductor.org/tag/visiumStitched See More Package Archives

Follow Installation instructions to use this package in your R session.

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