GeoMxWorkflows

DOI: 10.18129/B9.bioc.GeoMxWorkflows    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see GeoMxWorkflows.

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

Bioconductor version: 3.15

Workflows for use with NanoString Technologies GeoMx Technology. Package provides bioconductor focused workflows for leveraging existing packages (e.g. GeomxTools) to process, QC, and analyze the data.

Author: Jason Reeves [cre, aut], Prajan Divakar [aut], Nicole Ortogero [aut], Maddy Griswold [aut], Zhi Yang [aut], Stephanie Zimmerman [aut], Rona Vitancol [aut], Henderson David [aut]

Maintainer: Jason Reeves <jreeves at nanostring.com>

Installation

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

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

BiocManager::install("GeoMxWorkflows")

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("GeoMxWorkflows")

 

HTML	R Script	Analyzing GeoMx-NGS Data with GeomxTools
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpressionWorkflow, ImmunoOncologyWorkflow, SpatialWorkflow, Workflow
Version	1.2.0
License	MIT
Depends	R (>= 4.0), NanoStringNCTools, GeomxTools
Imports	Biobase, S4Vectors, rjson, readxl, EnvStats, dplyr, reshape2, methods, utils, stats, data.table, outliers, BiocGenerics, ggplot2, ggrepel, ggforce, cowplot, scales, umap, Rtsne, pheatmap, BiocStyle
LinkingTo
Suggests	rmarkdown, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package	GeoMxWorkflows_1.2.0.tar.gz
Windows Binary
macOS Binary (x86_64)
Source Repository	git clone https://git.bioconductor.org/packages/GeoMxWorkflows
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GeoMxWorkflows
Package Short Url	https://bioconductor.org/packages/GeoMxWorkflows/
Package Downloads Report	Download Stats