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 (3.20)
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("standR")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | DifferentialExpression, ExperimentHubSoftware, GeneExpression, Normalization, QualityControl, Software, Spatial, Transcriptomics |
Version | 1.9.3 |
In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
System Requirements | |
URL | https://github.com/DavisLaboratory/standR |
Bug Reports | https://github.com/DavisLaboratory/standR/issues |
See More
Suggests | knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | standR_1.9.3.tar.gz |
Windows Binary | standR_1.9.3.zip |
macOS Binary (x86_64) | standR_1.9.3.tgz |
macOS Binary (arm64) | standR_1.9.3.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 |