standR

DOI: 10.18129/B9.bioc.standR    

Spatial transcriptome analyses of Nanostring's DSP data in R

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	standR_introduction
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, ExperimentHubSoftware, GeneExpression, Normalization, QualityControl, Software, Spatial, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 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, mclustcomp
LinkingTo
Suggests	knitr, ExperimentHub, rmarkdown, scater, uwot, ggalluvial, ggpubr, ggrepel, cluster, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/DavisLaboratory/standR
BugReports	https://github.com/DavisLaboratory/standR/issues
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_1.0.0.tar.gz
Windows Binary	standR_1.0.0.zip
macOS Binary (x86_64)	standR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/standR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/standR
Package Short Url	https://bioconductor.org/packages/standR/
Package Downloads Report	Download Stats