BIOSZEN

Biological data analysis and visualization in R/Shiny
From data import to reproducible plots, statistics, metadata, and bundle exports.

IMPORTANT: For the most complete workflow, use Platemap + Curves input mode (Datos + PlotSettings + well-based curves).

TIP: If your dataset is large, start with .csv in Load Data and keep metadata as .xlsx.

Table of Contents

• Why BIOSZEN
• Core Capabilities
• Quick Start
• Choose the Right Input Mode
• Recommended Workflow
• Visual Gallery
• Common User Scenarios
• Documentation
• Troubleshooting
• Citation
• License

Why BIOSZEN

BIOSZEN is an R package with a modular Shiny app focused on biological experiment analysis. It helps you go from raw data to publication-ready visualizations while preserving reproducibility through metadata and bundle exports.

Core Capabilities

• Plot families: Boxplot, Barplot, Violin, Curves, Stacked, Correlation, Heatmap, Correlation Matrix.
• Statistical workflows: normality checks, significance testing, post hoc comparisons, p-value correction.
• Control-based normalization with replicate-aware behavior.
• Biological and technical replicate QC (manual + automatic strategies).
• Composition panel for multi-plot layouts and export (PNG, PDF, PPTX).
• Reproducibility features: metadata export/import and ZIP bundles.
• Growth module with extracted metrics: uMax, doub_time, lag_time, AUC, ODmax, and related fields.

Quick Start

1. Install R (>= 4.1).
2. Open this project folder.
3. Run one of the following:

Rscript app.R

Or inside R:

BIOSZEN::run_app()

4. Open the local URL shown in the console.

NOTE: On first launch, dependencies may be installed into a local R_libs directory. Keep this folder to avoid reinstalling packages.

Choose the Right Input Mode

• Platemap + Curves (recommended)
  Use it when: You need full plotting + stats + replicate/QC workflows.
  Required files: Datos + PlotSettings workbook, plus curves file (Time + wells).

• Grouped parameters
  Use it when: You only need parameter plots/statistics.
  Required files: Grouped parameter workbook in Load Data.

• Summary (Mean/SD/N)
  Use it when: Raw replicate rows are not available.
  Required files: Summary workbook with dedicated summary sheets.

• CSV mode
  Use it when: Dataset is large and you want lighter IO.
  Required files: .csv for data and/or curves; metadata still .xlsx.

Recommended Workflow

1. Load primary file in Load Data.
2. Optionally load curves in Load Curves.
3. Apply filters (group/media/replicate).
4. Choose plot type and visual settings.
5. Optionally normalize by control.
6. Run statistics and significance annotation.
7. Export plot/data/statistics/metadata/bundle.

CAUTION: If curves do not align with your groups, verify the Well mapping in platemap and the curves column names (A1, A2, etc.).

Visual Gallery

App Screens

Plot Examples

Common User Scenarios

I only have summary tables

• Use Summary (Mean/SD/N) mode.
• Focus on parameter visualization and supported statistical paths.
• Expect some normality/non-parametric options to be limited if raw observations are unavailable.

I need stronger replicate quality control

• Use BiologicalReplicate and TechnicalReplicate columns.
• Start with manual include/exclude.
• Then apply IQR filtering and Keep-N reproducibility filters.

I need reproducible, shareable output

• Export metadata after configuring your analysis.
• Export bundle ZIP at the end.
• Re-import metadata in a new session to restore state.

Documentation

• Main English manual: inst/app/www/MANUAL_EN.md
• Main Spanish manual: inst/app/www/MANUAL_ES.md
• PDF manuals:
  • inst/app/www/MANUAL_EN.pdf
  • inst/app/www/MANUAL_ES.pdf
• Input templates: inst/app/www/reference_files/

Reference templates include:

• Ejemplo_platemap_parametros.xlsx
• Ejemplo_curvas.xlsx
• Ejemplo_parametros_agrupados.xlsx
• Ejemplo_input_summary_mean_sd.xlsx

Troubleshooting

• Rscript not found
  Quick check: Install R and ensure Rscript is on PATH (or run with full executable path).

• Upload rejected
  Quick check: Verify required sheet names and column names.

• No plot shown
  Quick check: Confirm selected parameter/group still exists after filters.

• Stats unavailable
  Quick check: Check whether your input mode supports the selected statistical route.

• Slow performance
  Quick check: Reduce selected parameters and disable heavy overlays.

Citation

Szenfeld, B. (2026). BIOSZEN (2.0.1). Zenodo. https://doi.org/10.5281/zenodo.18217522

License

GPL-3.0