SpatialOmicsOverlay
This is the development version of SpatialOmicsOverlay; for the stable release version, see SpatialOmicsOverlay.
Spatial Overlay for Omic Data from Nanostring GeoMx Data
Bioconductor version: Development (3.23)
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 "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SpatialOmicsOverlay")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (2.5 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, BiocStyle, 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SpatialOmicsOverlay |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpatialOmicsOverlay |
| Package Short Url | https://bioconductor.org/packages/SpatialOmicsOverlay/ |
| Package Downloads Report | Download Stats |