SpatialOmicsOverlay

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Bioconductor version: 3.23 · Package version: 1.12.0

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	234
Source branch	RELEASE_3_23
biocViews	CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization

Documentation

Introduction to SpatialOmicsOverlay

Download

Source package

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