DOI: 10.18129/B9.bioc.standR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see standR.

Spatial transcriptome analyses of Nanostring's DSP data in R

Bioconductor version: 3.16

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>

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


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biocViews DifferentialExpression, ExperimentHubSoftware, GeneExpression, Normalization, QualityControl, Software, Spatial, Transcriptomics
Version 1.2.2
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
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
Suggests knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0)
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