# 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](#why-bioszen)
- [Core Capabilities](#core-capabilities)
- [Quick Start](#quick-start)
- [Choose the Right Input Mode](#choose-the-right-input-mode)
- [Recommended Workflow](#recommended-workflow)
- [Visual Gallery](#visual-gallery)
- [Common User Scenarios](#common-user-scenarios)
- [Documentation](#documentation)
- [AI Skill for Input Preparation](#ai-skill-for-input-preparation)
- [Troubleshooting](#troubleshooting)
- [Citation](#citation)
- [License](#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:
```bash
Rscript app.R
```
Or inside R:
```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
