GeoMxWorkflows

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see GeoMxWorkflows.

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

Bioconductor version: 3.21

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")
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

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Details

biocViews GeneExpressionWorkflow, ImmunoOncologyWorkflow, SpatialWorkflow, Workflow

Version 1.14.0

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

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Suggests rmarkdown, knitr

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Package Archives

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

Source Package GeoMxWorkflows_1.14.0.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/

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