Changelog • perturbplanapp

perturbplanApp 0.1.1

Updated perturbplan dependency from v0.3.0 to v0.3.1.
Updated custom pilot data validation to match library_estimation() format.
Fixed deployment issue where pkgload, desc, and pkgbuild were dropped from manifest.
Updated 15 dependency packages to latest versions.

Full integration with perturbplan package (v0.3.1) for real-time power analysis and experimental optimization.
Constraint-driven workflow supporting 11 design scenarios: 5 power-only and 6 power+cost optimization workflows.
Three analysis engines: standard power analysis, cost minimization, and constrained optimization.
Interactive Plotly visualizations for all workflow scenarios with log-scale axes for cells and reads parameters.
Dual-workflow architecture: sidebar-based configuration (Phase 1) with slider overrides for real-time parameter adjustment (Phase 2).
Support for both Perturb-seq and TAP-seq assay types with assay-aware parameter labels and transformations.
Custom pilot data upload with validation for Perturb-seq experiments (RDS format).
Built-in K562 reference expression data for quick-start analysis.
Custom gene list upload functionality.
Excel export of analysis results including parameter settings and pilot data.
PDF export for publication-ready plots with legend annotations.
Comprehensive tooltip system providing parameter descriptions and guidance.
Progressive disclosure UI with collapsible sidebar sections.
pkgdown documentation site with launch button and app schematic.

Slider-adjustable badges on sidebar inputs with widened sidebar layout.
Two-row slider layout with responsive design for parameter adjustment.
Solution table with bold formatting for varying and optimizing parameters.
Diamond annotations marking optimal solutions on plots.
Cost budget horizontal lines on constrained optimization plots.
Blur-based input clamping for all numeric parameters.
MOI=1 control group logic with explanatory text.
Assay-aware Expression threshold labeling (TPM for Perturb-seq, UMIs/cell for TAP-seq).

Fixed Expression threshold not freezing in Phase 2 sidebar.
Fixed app crash when MOI field is cleared.
Fixed fold change selection logic to choose value closest to 1.
Fixed constrained minimization plot to use points instead of duplicate lines.
Corrected MOI value in control group description.
Fixed layout issue causing results panels to shift to bottom.
Added informative error when no designs meet cost budget in constrained minimization.

Golem framework architecture with modular Shiny components.
5-layer parameter naming standardization (UI, Config, API, Processing, Display).
Component library with 283 semantic CSS components.
118 passing tests with comprehensive coverage.
Deployment via Posit Connect Cloud with auto-deployment from dev branch.