The GeoMxTools package contains tools for analyzing data from NanoString GeoMx Digital Spatial Profiler (DSP). It provides functions to read, quality control (QC) and normalize starting from Nanostring DCC and PKC files generated from the NanoString GeoMx DSP.
It contains the definition of the NanoStringGeoMxSet class which inherits from Biobase’s ExpressionSet class and NanoStringRCCSet class.
https://bioconductor.org/packages/release/bioc/html/GeomxTools.html
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install(version="release")
BiocManager::install("GeomxTools")install.packages("devtools")
library("devtools")
devtools::install_github("Nanostring-Biostats/GeomxTools",
build_vignettes = TRUE, ref = "dev")To get started, it is recommended to begin with the example workflow:
GeoMx Workflow
To learn how to start developing with GeoMxTools, view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GeomxTools")The release version on Bioconductor is the stable version. https://bioconductor.org/packages/release/bioc/html/GeomxTools.html
The devel version on Bioconductor is upstream of master on GitHub. It is under active development and no guarantee is made on usability at any given time.
The dev branch on GitHub is under active development and no guarantee is made on usability at any given time.
Ortogero, N.; Yang, Z.; Vitancol, R.; Griswold, M.; Henderson, D. GeomxTools: NanoString GeoMx Tools. R Package Version 2.1.1. NanoString Technologies Inc.; Seattle, WA 98109, USA. 2021.
This project is licensed under the MIT license.