bioconductor-standr

name

bioconductor-standr

description

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.

standR

Workflows

Standard Workflow

Perform quality control, TMM normalization, and RUV4 batch correction on NanoString GeoMx DSP data.

library(standR)
library(SpatialExperiment)
library(limma)
library(ExperimentHub)

# Load data
eh <- ExperimentHub()
countFile <- eh[["EH7364"]]
sampleAnnoFile <- eh[["EH7365"]]
featureAnnoFile <- eh[["EH7366"]]

spe <- readGeoMxcountFile sampleAnnoFile featureAnnoFile  featureAnnoFile rmNegProbe  


colDatasperegions  paste0colDatasperegioncolDataspeSegmentLabel  
  . gsub. 
  paste0colDataspepathology 
  . gsub.

spe  addPerROIQCspe rm_genes  
spe  sperownamescolDataspecolDataspelib_size  


colDataspebiology  paste0colDataspedisease_status  colDatasperegions
spe_tmm  geomxNormspe method  


spe  findNCGsspe batch_name   top_n  
spe_ruv  geomxBatchCorrectionspe factors   NCGs  metadataspeNCGs k