Developer Notes

Purpose of This Section

This section is for documenting technical decisions, challenges, and solutions encountered during your project. These notes are valuable for:

• Future you (who will forget why certain decisions were made)
• Collaborators who join the project later
• People coming from your publication who want to reproduce your work
• Anyone who might want to extend your research

What to Document

Design Decisions

Document important decisions about your project's architecture, algorithms, or methodologies:

## Choice of RNA-Seq Analysis Pipeline

[2025-04-25] We chose the kallisto over STAR pipeline for the following reasons:
    1. The CCLE dataset is very large, and kallisto is faster for quantifying large datasets
    2. GDSC used kallisto, so we can compare our results with theirs

Technical Challenges

Record significant problems you encountered and how you solved them

## Sample Name Format Issue

[2025-04-25] We encountered a problem with sample name formats between the CCLE and GDSC datasets.
    The CCLE dataset uses "BRCA-XX-XXXX" format, while the GDSC dataset uses "BRCA-XX-XXXX-XX".
    We had to write a script to remove the last two characters from the sample names in the GDSC dataset.

Dependencies and Environment

Document specific version requirements or compatibility issues:

## Critical Version Dependencies

[2025-04-25] SimpleITK 2.4.1 introduced a bug that flips images, so we froze version 2.4.0

Best Practices

• Date your entries when appropriate
• Link to relevant code files or external resources
• Include small code snippets when helpful
• Note alternatives you considered and why they were rejected
• Document failed approaches to prevent others from repeating mistakes
• Update notes when major changes are made to the approach