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GeomxTools

This is the development version of GeomxTools; for the stable release version, see GeomxTools.

NanoString GeoMx Tools


Bioconductor version: Development (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 nanostring.com>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GeomxTools")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GeomxTools")
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
NEWS Text
LICENSE Text

Details

biocViews CellBasedAssays, DataImport, ExperimentalDesign, GeneExpression, Normalization, ProprietaryPlatforms, Proteomics, RNASeq, Sequencing, Software, Spatial, Transcription, Transcriptomics, mRNAMicroarray
Version 3.7.2
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
URL
See More
Suggests rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment(>= 1.4.0), SpatialDecon, patchwork
Linking To
Enhances
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_3.7.2.tar.gz
Windows Binary GeomxTools_3.7.2.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/GeomxTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeomxTools
Bioc Package Browser https://code.bioconductor.org/browse/GeomxTools/
Package Short Url https://bioconductor.org/packages/GeomxTools/
Package Downloads Report Download Stats