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GeomxTools (development version)

GeomxTools

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

NanoString GeoMx Tools

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DOI: 10.18129/B9.bioc.GeomxTools

Bioconductor version: Development (3.23)

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 "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBasedAssays, DataImport, ExperimentalDesign, GeneExpression, Normalization, ProprietaryPlatforms, Proteomics, RNASeq, Sequencing, Software, Spatial, Transcription, Transcriptomics, mRNAMicroarray

Version 3.15.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 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

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_3.15.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64) GeomxTools_3.15.0.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/

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