SpatialOmicsOverlay
Spatial Overlay for Omic Data from Nanostring GeoMx Data
Bioconductor version: Release (3.19)
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 "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization |
Version | 1.4.0 |
In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
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 | |
URL |
See More
Suggests | knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf |
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 | SpatialOmicsOverlay_1.4.0.tar.gz |
Windows Binary | SpatialOmicsOverlay_1.4.0.zip |
macOS Binary (x86_64) | SpatialOmicsOverlay_1.4.0.tgz |
macOS Binary (arm64) | SpatialOmicsOverlay_1.4.0.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 |
Old Source Packages for BioC 3.19 | Source Archive |