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Bioconductor - GeoMxWorkflows (development version)

GeoMxWorkflows

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

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews GeneExpressionWorkflow, ImmunoOncologyWorkflow, SpatialWorkflow, Workflow Version 1.15.0 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 See More Suggests rmarkdown, knitr Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Package Archives

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

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