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# 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 <> ### Install the release version from Bioconductor ``` r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(version="release") BiocManager::install("GeomxTools") ``` ### Install the development version from GitHub ``` r 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: ``` r browseVignettes("GeomxTools") ``` ## Branches The release version on Bioconductor is the stable version. <> 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](LICENSE).