Registration Open for Bioc2024 July 24-26


NanoString GeoMx Tools

Bioconductor version: Release (3.19)

Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included.

Author: Maddy Griswold [cre, aut], Nicole Ortogero [aut], Zhi Yang [aut], Ronalyn Vitancol [aut], David Henderson [aut]

Maintainer: Maddy Griswold <mgriswold at>

Citation (from within R, enter citation("GeomxTools")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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:

Coercion of GeoMxSet to Seurat and SpatialExperiment Objects HTML R Script
Developer Introduction to the NanoStringGeoMxSet HTML R Script
Protein data using GeomxTools HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, DataImport, ExperimentalDesign, GeneExpression, Normalization, ProprietaryPlatforms, Proteomics, RNASeq, Sequencing, Software, Spatial, Transcription, Transcriptomics, mRNAMicroarray
Version 3.8.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT
Depends R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors
Imports BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject
System Requirements
See More
Suggests rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment(>= 1.4.0), SpatialDecon, patchwork
Linking To
Depends On Me GeoMxWorkflows
Imports Me GeoDiff, SpatialDecon, SpatialOmicsOverlay
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GeomxTools_3.8.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) GeomxTools_3.8.0.tgz
macOS Binary (arm64) GeomxTools_3.8.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats