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 |