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Bioconductor - standR

standR

This is the released version of standR; for the devel version, see standR.

Spatial transcriptome analyses of Nanostring's DSP data in R

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-9487-9305 , Dharmesh D Bhuva [aut] ORCID: 0000-0002-6398-9157 , Ahmed Mohamed [aut]

Maintainer: Ning Liu <ning.liu at adelaide.edu.au>

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

To install this package, start R (version "4.5") 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")
Details biocViews DifferentialExpression, ExperimentHubSoftware, GeneExpression, Normalization, QualityControl, Software, Spatial, Transcriptomics Version 1.12.0 In Bioconductor since BioC 3.15 (R-4.2) (3 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 Package Archives

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

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