Core documents
01
Onboarding
What this part of the lab does, and guidance for how to get started.
02
Computing Environment
Hardware requirements, software installation, HPC access, and a setup checklist to complete in your first week.
03
Git & GitHub Workflow
How to manage, share, and version code using the lab's fork-based workflow and daily commit practices.
04
Coding Standards
Standards for R scripts, Rmarkdown, helper functions, R packages, and publication-ready code.
05
Data Management
How data is stored, organized, documented, and preserved across the lab's three storage locations.
06
AI Tools & Claude
How to use AI effectively, honestly, and without losing your own judgment. Includes CLAUDE.md and Skills files.
07
Ethics & Teamwork
Authorship, data integrity, credit, communication, and lab culture.
08
Publication & Archiving
Figure standards, code release, data deposition, and project archiving at publication.
Appendices
How to use this manual
Read Documents 01 and 02 in your first week, in order. They cover the lab's context and the practical setup required to get started. Documents 03 through 08 can be read in any order and referred back to as needed.
Each document is standalone: you can link directly to any section using the URL and the anchor in the sidebar. The manual will be updated as the lab's tools and practices evolve.
If you have questions not addressed here, ask on Slack or bring them to your weekly 1:1.