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

Documentation website

Practical Transcriptomics with R

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

Languages & Tools

R Quarto Bioconductor

Packages

GEOquery tidyverse limma edgeR sva ggplot2

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

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

Completed:

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

Planned:

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