This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

standR

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

Spatial transcriptome analyses of Nanostring's DSP data in R

Bioconductor version: Development (3.18)

standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.

Author: Ning Liu [aut, cre] , Dharmesh D Bhuva [aut] , Ahmed Mohamed [aut]

Maintainer: Ning Liu <liu.n at wehi.edu.au>

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

Installation

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

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

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

BiocManager::install("standR")

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("standR")
standR_introduction HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, ExperimentHubSoftware, GeneExpression, Normalization, QualityControl, Software, Spatial, Transcriptomics
Version 1.5.2
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports dplyr, SpatialExperiment(>= 1.5.2), SummarizedExperiment, SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2, tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics, grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq
Linking To
Suggests knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0)
System Requirements
Enhances
URL https://github.com/DavisLaboratory/standR
Bug Reports https://github.com/DavisLaboratory/standR/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package standR_1.5.2.tar.gz
Windows Binary standR_1.5.2.zip
macOS Binary (x86_64) standR_1.5.2.tgz
macOS Binary (arm64) standR_1.5.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/standR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/standR
Bioc Package Browser https://code.bioconductor.org/browse/standR/
Package Short Url https://bioconductor.org/packages/standR/
Package Downloads Report Download Stats