GeomxTools

DOI: 10.18129/B9.bioc.GeomxTools  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see GeomxTools.

NanoString GeoMx Tools

Bioconductor version: 3.17

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 nanostring.com>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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
Text		LICENSE

Details

biocViews	CellBasedAssays, DataImport, ExperimentalDesign, GeneExpression, Normalization, ProprietaryPlatforms, Proteomics, RNASeq, Sequencing, Software, Spatial, Transcription, Transcriptomics, mRNAMicroarray
Version	3.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (2.5 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
LinkingTo
Suggests	rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment(>= 1.4.0), SpatialDecon, patchwork
SystemRequirements
Enhances
URL
Depends On Me	GeoMxWorkflows
Imports Me	GeoDiff, SpatialDecon, SpatialOmicsOverlay
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GeomxTools_3.4.0.tar.gz
Windows Binary	GeomxTools_3.4.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)	GeomxTools_3.3.0.tgz
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