SpatialOmicsOverlay

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Bioconductor version: 3.24 · Package version: 1.13.0

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.

Installation

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

BiocManager::install("SpatialOmicsOverlay")

Details

Maintainer	Maddy Griswold <mgriswold@nanostring.com>
Author	Maddy Griswold [cre, aut], Megan Vandenberg [ctb], Stephanie Zimmerman [ctb]
License	MIT
Downloads rank	415
Source branch	devel
biocViews	CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization

Documentation

Introduction to SpatialOmicsOverlay

Download

Follow the installation instructions to use this package in your R session.

Source package	SpatialOmicsOverlay_1.13.0.tar.gz
Windows binary (x86_64)	SpatialOmicsOverlay_1.13.0.zip
macOS binary (arm64)	SpatialOmicsOverlay_1.13.0.tgz
macOS binary (x86_64)	SpatialOmicsOverlay_1.13.0.tgz

Dependencies

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

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