NEWS

CySA 0.99.8

Added hover-over tooltips (title attributes) to every non-obvious control in the clusterSelector() sidebar and body panels.
Added inline helpText() explanations for subtle controls such as selection mode, scatter auto-zoom percentile, and dimension-reduction settings.
Added selection hints to all plot outputs that support click/lasso selection.
Extended roxygen comments for all UI builder helpers in R/ui-helpers.R.

Fixed remaining indentation outliers (hanging indents and manually edited blocks) so all R source lines use multiples of 4 spaces.

Converted R source files from 2-space to 4-space indentation to conform to Bioconductor style guidelines.

Replaced <<- with shiny::reactiveVal() for app state.
Removed debug cat()/print() calls; kept print() only inside PDF device context.
Applied styler formatting and wrapped selected long lines.

Initial Bioconductor submission of CySA, an interactive Shiny dashboard for selecting and visualizing clusters from flow-cytometry data stored in SingleCellExperiment objects.
clusterSelector() returns a Shiny app object that can be launched with shiny::runApp().
prepClusterSelectorData() subsamples a SingleCellExperiment and builds the inputs required by clusterSelector().
plotSOMScatter() and plotCytoScatter() provide ggplot2-based SOM and scatter visualizations.

Replaced broad package-level @import directives with targeted @importFrom roxygen tags to reduce namespace masking.
Removed the archived ggthemr dependency; theming now uses theme_minimal() and explicit scale_*_manual() scales.
Added NEWS.md, expanded README.Rmd, and a package vignette.