GeomxTools

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see GeomxTools.

NanoString GeoMx Tools


Bioconductor version: 3.14

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]

Maintainer: Nicole Ortogero <nortogero at nanostring.com>

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

Installation

To install this package, start R (version "4.1") 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")
Developer Introduction to the NanoStringGeoMxSet HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CellBasedAssays, DataImport, ExperimentalDesign, GeneExpression, Normalization, ProprietaryPlatforms, Proteomics, RNASeq, Sequencing, Software, Transcription, Transcriptomics, mRNAMicroarray
Version 2.0.0
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, outliers, lmerTest, dplyr
System Requirements
URL
See More
Suggests rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph
Linking To
Enhances
Depends On Me GeoMxWorkflows
Imports Me GeoDiff, SpatialDecon
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_2.0.0.tar.gz
Windows Binary GeomxTools_2.0.0.zip
macOS 10.13 (High Sierra) GeomxTools_2.0.0.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
Old Source Packages for BioC 3.14 Source Archive