Package index • Coereba

All functions

Coereba_App(): Deploy a Shiny app to modify the estimated gate cutoff placement.

Coereba_Comparison(): Compares two Coereba populations to find difference, returning either data or a plot of the marker expressions

Coereba_FCSExport(): Takes Coereba Output and generates both .fcs file and a dictionary.

Coereba_FCS_Reversal(): Handles Description Digging for Dictionary Reversal going FCS to data

Coereba_GateCutoffs(): Function to guess the gate cutoff values

Coereba_MarkerExpressions(): Generate overall marker expressions across Coereba clusters,

Coereba_Processing(): Takes Utility_Coereba output, plus additional metadata,and returns as a Bioconductor Summarized Experiment object

Coereba_UpdateGates(): Update a gate cutoff csv with the Coereba_App edits

Utility_Behemoth(): From a data.frame, runs stats on column of interest, and returns the ggplot for it.

Utility_Coereba(): Runs Coereba for Dichotomized Gating Annotation

Utility_Heatmap(): Produces a Coereba Heatmap showing Coereba Clusters by Markers

Utility_LongitudinalBehemoth(): Scales up Utility_Behemoth to handle two factors on the x-axis, allowing for longitudinal plotting

Utility_MarkerPlots(): Takes Coereba_MarkerExpressions data.frame and returns Marker Expression Beeswarm plots

Utility_Stats(): Normality Test followed by t-test/Anova