Practical Transcriptomics with R

Educational workflow for transcriptomic preprocessing, GEO data exploration and reproducible bioinformatics analysis

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🌐 Live Project

Documentation website

Practical Transcriptomics with R

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📌 Project Summary

Tutorial-style transcriptomics workflow designed to transform raw GEO datasets into analysis-ready data.

Key concepts covered::

• GEO data retrieval
• Metadata filtering
• Transcriptomic preprocessing
• Quality control
• Normalization strategies
• Reproducible workflows
• Data preparation for downstream analyses

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🛠 Tech Stack

Languages & Tools

R Quarto Bioconductor

Packages

GEOquery tidyverse limma edgeR sva ggplot2

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🔬 Workflow

GEO datasets
      ↓
Metadata exploration
      ↓
Sample filtering
      ↓
Quality control
      ↓
Normalization
      ↓
Preprocessed dataset

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📂 Repository Structure

.
├── Searching_data/
├── Preprocessing_data/
├── index.qmd
├── custom.css
└── README.md

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🚧 Current Status

Completed:

✔ GEO retrieval
✔ Metadata exploration
✔ Sample filtering
✔ QC visualization
✔ Normalization concepts

Planned:

⬜ Differential expression
⬜ Batch correction
⬜ RNA-seq workflows
⬜ ML applications