NEWS

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NOVA 0.1.6

Example Dataset Update

• Replaced private example data (MEA022b/MEA022c, Mavs KO genotypes) with publicly available WT neuron data (MEA012, MEA013)
• Example dataset now uses WT neurons with neuronal agonist treatments: PBS, KCl, DHPG, Gabazine (MEA012) and PBS, AMPA, KA, DHPG, Gabazine (MEA013)
• Updated all example scripts (nova_quickstart.R, 01_compute.R, 02_plot.R, mea-analysis-example.Rmd) to reflect WT-only dataset structure
• GENOTYPE_COLUMN now defaults to NULL in quickstart for WT-only datasets
• Removed compiled HTML and figure outputs generated from private dataset

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NOVA 0.1.1 (2025-10-16)

CRAN Resubmission Fixes

• Removed all commented code from examples and function bodies
• Fixed DESCRIPTION to spell out Multi-Electrode Array (MEA) without quotes
• Added newlines at end of all R source files
• Fixed parse errors in documentation examples

Initial CRAN Release

This is the first release of NOVA (Neuroactivity Omics Visualization and Analysis), a comprehensive toolkit for analyzing and visualizing Multi-Electrode Array (MEA) data.

Main Features

• Data Processing: Flexible MEA data processing with automatic structure discovery

  • discover_mea_structure(): Automatically detects data structure
  • process_mea_flexible(): Processes MEA data with quality filtering options
  • handle_missing_values(): Multiple strategies for handling missing data

• Principal Component Analysis:

  • pca_analysis_enhanced(): Comprehensive PCA with visualization
  • analyze_pca_variable_importance_general(): Variable importance analysis
  • plot_pca_trajectories_general(): Trajectory visualization across conditions

• Heatmap Visualization:

  • create_mea_heatmaps_enhanced(): Publication-ready heatmaps with multiple scaling options
  • Support for hierarchical clustering and custom annotations

• Utility Functions: Helper functions for data manipulation, scaling, and color schemes

Documentation

• Comprehensive function documentation with examples
• Vignettes demonstrating typical workflows
• Support for various MEA data formats