Apply Normalization Methods to Multiplexed Images

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Documentation for package ‘mxnorm’ version 1.0.3

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

Help Pages

mx_dataset	Generates mx_dataset
mx_normalize	Normalizes multiplexed data
mx_sample	Sample multiplexed dataset for 'mxnorm'.
plot_mx_density	Visualize marker density before/after normalization by marker and slide
plot_mx_discordance	Visualize Otsu discordance scores by marker and slide
plot_mx_proportions	Visualize variance proportions by marker and table
plot_mx_umap	Visualize UMAP dimension reduction algorithm
print.summary.mx_dataset	Extension of 'print' S3 method to print 'summary.mx_dataset' objects
run_otsu_discordance	Calculate Otsu discordance scores using specified threshold for an 'mx_dataset' object.
run_reduce_umap	Run UMAP dimension reduction algorithm on an 'mx_dataset' object.
run_var_proportions	Run random effects modeling on 'mx_dataset' object to determine proportions of variance at the slide level
summary.mx_dataset	Extension of 'summary' S3 method to summarize 'mx_dataset' objects