Spatial transcriptome analyses of Nanostring's DSP data in R

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Documentation for package ‘standR’ version 1.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
readGeoMxFromDGE	Import GeoMX DSP data into a spatial experiment object from DGEList object
spe2dge	Transfer SpatialExperiment object into DGEList object for DE analysis