visiumStitched
This is the development version of visiumStitched; to use it, please install the devel version of Bioconductor.
Enable downstream analysis of Visium capture areas stitched together with Fiji
Bioconductor version: Development (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:
Maintainer: Nicholas J. Eagles <nickeagles77 at gmail.com>
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")| Introduction to visiumStitched | HTML | R Script |
| Miscellaneous notes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GeneExpression, Software, Spatial, Transcription, Transcriptomics, Visualization |
| Version | 0.99.15 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| 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
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | visiumStitched_0.99.15.tar.gz |
| Windows Binary (x86_64) | visiumStitched_0.99.15.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/visiumStitched |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/visiumStitched |
| Bioc Package Browser | https://code.bioconductor.org/browse/visiumStitched/ |
| Package Short Url | https://bioconductor.org/packages/visiumStitched/ |
| Package Downloads Report | Download Stats |