GeoMxWorkflows
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GeoMxWorkflows.
GeoMx Digital Spatial Profiler (DSP) data analysis workflows
Bioconductor version: 3.16
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("GeoMxWorkflows")):
Installation
To install this package, start R (version "4.2") 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 | 1.4.0 |
| 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 |
| 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.
| Source Package | GeoMxWorkflows_1.4.0.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/ |
| Package Downloads Report | Download Stats |