GeoMxWorkflows

DOI: 10.18129/B9.bioc.GeoMxWorkflows    

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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")

 

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Details

biocViews GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow
Version 1.0.1
License MIT
Depends R (>= 4.1), 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_1.0.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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

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