# Apply Normalization Methods to Multiplexed Images

## Documentation for package ‘mxnorm’ version 1.1.0

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

## 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