standR: spatial transcriptomics analyses and decoding in R

The standR package provides a series of functions to assist different stages of the analysis of spatial transcriptomics data generated from the Nanostring's GeoMX DSP platforms. Most functions in the package is based on the infrastructure SpatialExperiment, see detials here.

See full guide at HERE

Latest news

standR 1.17.6

• Prepare SpatialDecon input from the existing logcounts assay on the linear scale, or recompute linear CPM from raw counts with recomputeCPM = TRUE. Expression and negative probes use matching background scaling.

standR 1.17.3

• Add readGeoMxFromDcc() to import DCC/PKC workflows directly into SpatialExperiment objects without requiring GeomxTools.

• Improve prepareSpatialDecon() so negative probes removed by readGeoMx(rmNegProbe = TRUE) can be read from metadata(spe)$NegProbes.

Overall workflow

Example data

The published GeoMX WTA data of diabetic kidney disease that we used in the vignette is available here.

Installation

Install the release version from Bioconductor

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

BiocManager::install("standR")

Install development version from GitHub

library(devtools)   
devtools::install_github("DavisLaboratory/standR")

Citation

To cite standR, plese cite the following article: https://doi.org/10.1093/nar/gkad1026 Much appreciated!