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SpatialOmicsOverlay
This is thedevelopment version of SpatialOmicsOverlay; for the stable release version, seeSpatialOmicsOverlay.
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("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 develBiocManager::install(version='devel')BiocManager::install("SpatialOmicsOverlay")For older versions of R, please refer to the appropriateBioconductor 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 | 1.11.0 |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | SpatialOmicsOverlay_1.11.0.tar.gz |
| Windows Binary (x86_64) | SpatialOmicsOverlay_1.11.0.zip |
| macOS Binary (x86_64) | SpatialOmicsOverlay_1.11.0.tgz |
| macOS Binary (arm64) | SpatialOmicsOverlay_1.11.0.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 |