🧬 OncoDex

OncoDex is a simple yet powerful web application for biomedical researchers and clinicians to upload, preview, and analyse experimental and clinical datasets. It provides quick access to summary statistics and basic visualisations to facilitate exploratory data analysis (EDA) — without writing code.

🧪 Final project for CS50x – Harvard's Introduction to Computer Science

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🚀 Features

• 📁 Upload multiple .csv datasets
• 👁️ Preview tabular data directly in the browser
• 📊 View summary statistics (mean, SD, min, max, etc.)
• 🧮 Automatically generate bar plots of means ± standard deviations for all numeric columns
• 🎨 Clean, responsive UI styled with custom CSS
• 🔐 Safe file handling and server-side validation

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🛠️ Tech Stack

Layer	Tool
Backend	Python + Flask
Frontend	HTML + Jinja2 Templates + CSS
Data	Pandas
Plotting	Matplotlib
Deployment	Localhost (Flask dev server)
File Storage	uploads/ folder (temp CSV storage)

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📦 Requirements

Create a virtual environment and install dependencies:

python3 -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate
pip install -r requirements.txt

requirements.txt

Flask==2.3.2
pandas==2.0.3
matplotlib==3.7.1
Werkzeug==2.3.7

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📁 Project Structure

OncoDex/
├── app.py                     # Flask app
├── requirements.txt
├── uploads/                   # Uploaded CSVs (temporary)
│   ├── dummy_data.csv
│   └── dummy_data2.csv
├── static/
│   └── styles.css             # Custom styling
├── templates/                 # HTML templates
│   ├── layout.html            # Base layout
│   ├── index.html             # Home
│   ├── upload.html            # Upload form
│   ├── upload_confirmation.html
│   ├── analyse.html           # Data preview and stats
│   └── about.html             # About section

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🧪 Usage

Start the app:

python app.py

Then open your browser and go to: 📍 http://127.0.0.1:5000

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🧭 Navigation

Page	URL Path	Description
Home	/	Welcome screen
Upload	/upload	Upload a CSV
Analyse	/analyse	Select and analyse uploaded CSVs
About	/about	Instructions & app overview

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📊 Example Output

After uploading a dataset, OncoDex automatically:

• Displays the first five rows
• Generates summary statistics (mean, std, min, max, etc.)
• Plots mean ± standard deviation for numeric columns (Rendered inline via base64-encoded PNG)

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📌 Why I Built This

I created OncoDex as a final project for CS50x to bring together key programming concepts:

• Routing and form handling in Flask
• File upload and sanitisation
• Data parsing and visualisation with Pandas/Matplotlib
• HTML templating with Jinja2
• Basic frontend styling with CSS

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✅ Possible Extensions

• 📈 Add scatterplots or histograms
• 📤 Export summary stats or plots as files
• 🔍 Add filtering/search for data columns
• 🔐 Integrate user authentication (login/logout)

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