SpatialOmicsOverlay

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see SpatialOmicsOverlay.

Spatial Overlay for Omic Data from Nanostring GeoMx Data

DOI: 10.18129/B9.bioc.SpatialOmicsOverlay

Bioconductor version: 3.18

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>

Citation (from within R, enter citation("SpatialOmicsOverlay")):

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")

Introduction to SpatialOmicsOverlay HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization

Version 1.2.1

In Bioconductor since BioC 3.17 (R-4.3) (1 year)

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

System Requirements

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Suggests knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf

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