visiumStitched
This is the released version of visiumStitched; for the devel version, see visiumStitched.
Enable downstream analysis of Visium capture areas stitched together with Fiji
Bioconductor version: Release (3.23)
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 hexagonal 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] 
, Leonardo Collado-Torres [ctb]
Maintainer: Nicholas J. Eagles <nickeagles77 at gmail.com>
citation("visiumStitched")):Nicholas J. Eagles. visiumStitched: Enable downstream analysis of Visium capture areas stitched together with Fiji. doi:10.18129/B9.bioc.visiumStitched, R package version 1.4.0, https://bioconductor.org/packages/visiumStitched.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("visiumStitched")| Miscellaneous notes | HTML | R Script |
| Introduction to visiumStitched | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneExpression, Software, Spatial, Transcription, Transcriptomics, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4), SpatialExperiment |
| Imports | BiocBaseUtils, BiocGenerics, clue, 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
| Suggests | BiocFileCache, BiocStyle, ggplot2, knitr, RefManageR, rmarkdown, sessioninfo, Seurat, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | visiumStitched_1.4.0.tar.gz |
| Windows Binary (x86_64) | visiumStitched_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | visiumStitched_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | visiumStitched_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/visiumStitched |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/visiumStitched |
| Package Short Url | https://bioconductor.org/packages/visiumStitched/ |
| Package Downloads Report | Download Stats |