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GeoMxWorkflows

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

Bioconductor version: Release (3.17)

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>

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

Installation

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

Details

biocViews GeneExpressionWorkflow, ImmunoOncologyWorkflow, SpatialWorkflow, Workflow
Version 1.6.0
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
Linking To
Suggests rmarkdown, knitr
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Package Archives

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

Source Package GeoMxWorkflows_1.6.0.tar.gz
Windows Binary
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/
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