DOI: 10.18129/B9.bioc.GeomxTools  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GeomxTools.

NanoString GeoMx Tools

Bioconductor version: 3.16

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

Maintainer: Nicole Ortogero <nortogero at>

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


To install this package, start R (version "4.2") and enter:

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


For older versions of R, please refer to the appropriate Bioconductor release.


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


biocViews CellBasedAssays, DataImport, ExperimentalDesign, GeneExpression, Normalization, ProprietaryPlatforms, Proteomics, RNASeq, Sequencing, Software, Spatial, Transcription, Transcriptomics, mRNAMicroarray
Version 3.2.0
In Bioconductor since BioC 3.13 (R-4.1) (2 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
Suggests rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment(>= 1.4.0), SpatialDecon, patchwork
Depends On Me GeoMxWorkflows
Imports Me GeoDiff, SpatialDecon
Suggests Me
Links To Me
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