Bioconductor version: Release (3.17)
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")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SpatialOmicsOverlay")
HTML | R Script | Introduction to SpatialOmicsOverlay |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | CellBasedAssays, DataImport, DataRepresentation, GeneExpression, ProprietaryPlatforms, Proteomics, RNASeq, Software, Spatial, Transcription, Transcriptomics, Visualization |
Version | 1.0.0 |
In Bioconductor since | BioC 3.17 (R-4.3) (< 6 months) |
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 |
LinkingTo | |
Suggests | knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | SpatialOmicsOverlay_1.0.0.tar.gz |
Windows Binary | SpatialOmicsOverlay_1.0.0.zip |
macOS Binary (x86_64) | SpatialOmicsOverlay_1.0.0.tgz |
macOS Binary (arm64) | SpatialOmicsOverlay_1.0.0.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 3.17 | Source Archive |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: