GeoMxTools

Overview

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.

Installation

Download the release version from Bioconductor

https://bioconductor.org/packages/release/bioc/html/GeomxTools.html

Install the release version from Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

BiocManager::install(version="release")

BiocManager::install("GeomxTools")

Install the development version from GitHub

install.packages("devtools")
library("devtools")
devtools::install_github("Nanostring-Biostats/GeomxTools", 
                         build_vignettes = TRUE, ref = "dev")

Documentation

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")

Branches

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.

Citation

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.

License

This project is licensed under the MIT license.