# Spatial transcriptome analyses of Nanostring's DSP data in R

## Documentation for package ‘standR’ version 1.17.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

addPerROIQC | Add QC statistics to the Spatial Experiment object
computeClusterEvalStats | Calculate statistics for evaluating batch correction
drawPCA | Compute and plot the results of a PCA analysis on gene expression data
drawPCA-method | Compute and plot the results of a PCA analysis on gene expression data
findBestK | Testing multiple K for RUV4 batch correction to find the best K.
findNCGs | Get negative control genes from each batch of the data
geomxBatchCorrection | Batch correction for GeoMX data
geomxNorm | Perform normalization to GeoMX data
plotClusterEvalStats | Compare and evaluate different batch corrected data with plotting.
plotDR | Compute and plot the results of any dimension reduction methods on gene expression data
plotDR-method | Compute and plot the results of any dimension reduction methods on gene expression data
plotGeneQC | Plot gene-wise QC plot
plotMDS | Compute and plot the results of a MDS analysis on gene expression data
plotMDS-method | Compute and plot the results of a MDS analysis on gene expression data
plotPairPCA | Plot pair-wise PCA plots for multiple dimensions
plotPCAbiplot | Plot PCA bi plot
plotRLExpr | Compute and plot relative log expression (RLE) values of gene expression data
plotRLExpr-method | Compute and plot relative log expression (RLE) values of gene expression data
plotROIQC | Plot Sample-wise QC plot
plotSampleInfo | Plot the user-defined meta data using alluvium plot
plotScreePCA | Plot the PCA scree plot.
prepareSpatialDecon | Preparing the inputs for SpatialDecon for doing deconvolution on spatial data
readGeoMx | Import GeoMX DSP data into a saptial experiment object from file paths
readGeoMxFromDcc | Import GeoMX DSP data from DCC files
readGeoMxFromDGE | Import GeoMX DSP data into a spatial experiment object from DGEList object
readGeoMxFromNanoStringGeoMxSet | Import GeoMX DSP data from a NanoStringGeoMxSet-like object
spe2dge | Transfer SpatialExperiment object into DGEList object for DE analysis