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 (3.22)
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 <ning.liu at adelaide.edu.au>
citation("standR")):
Installation
To install this package, start R (version "4.5") 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 | 1.13.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 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 | shinyDSP |
| 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_1.13.0.tar.gz |
| Windows Binary (x86_64) | standR_1.13.0.zip |
| macOS Binary (x86_64) | standR_1.13.0.tgz |
| macOS Binary (arm64) | standR_1.13.0.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 |