GeoMxWorkflows

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

Bioconductor version: Release (3.20)

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

Maintainer: Maddy Griswold <mgriswold at nanostring.com>

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

Installation

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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpressionWorkflow, ImmunoOncologyWorkflow, SpatialWorkflow, Workflow
Version	1.12.0
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, networkD3
System Requirements
URL

Suggests	rmarkdown, knitr
Linking To
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Depends On Me
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Package Archives

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

Source Package	GeoMxWorkflows_1.12.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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