SpatialOmicsOverlay

DOI: 10.18129/B9.bioc.SpatialOmicsOverlay  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SpatialOmicsOverlay.

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Bioconductor version: 3.17

Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.

Author: Maddy Griswold [cre, aut], Megan Vandenberg [ctb], Stephanie Zimmerman [ctb]

Maintainer: Maddy Griswold <mgriswold at nanostring.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SpatialOmicsOverlay")

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("SpatialOmicsOverlay")

 

HTML	R Script	Introduction to SpatialOmicsOverlay
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	MIT
Depends	R (>= 4.1.0)
Imports	S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats
LinkingTo
Suggests	knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SpatialOmicsOverlay_1.0.0.tar.gz
Windows Binary	SpatialOmicsOverlay_1.0.0.zip
macOS Binary (x86_64)	SpatialOmicsOverlay_1.0.0.tgz
macOS Binary (arm64)	SpatialOmicsOverlay_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpatialOmicsOverlay
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpatialOmicsOverlay
Bioc Package Browser	https://code.bioconductor.org/browse/SpatialOmicsOverlay/
Package Short Url	https://bioconductor.org/packages/SpatialOmicsOverlay/
Package Downloads Report	Download Stats