General

• Save files in Unicode (UTF-8), Unix (LF).
• Preferred editors are BBEdit, Sublime Text, Emacs, or vim.
• Indent with 4 spaces, auto-expand tabs.
• Maximum of 80 characters per line.
• snake_case for file names.
• Avoid abbreviations and acronyms whenever possible (e.g. identifier instead of id).
• Variables with single word acronyms should be lowercase (e.g. rna instead of RNA).

Bash

• Follow the Google Shell style guide.

Python

• Follow the PEP 8 guidelines.
• snake_case for variable names.

R

• Write code using RStudio. It has great built-in support for proper indentation and RMarkdown.
• Follow the Bioconductor style guide for package development.
• Hadley’s style guide is also a useful general style reference.
• Periods are reserved for base R definitions.
• Use descriptive variable names.
• Avoid naming variables after functions, whenever possible.
• Use nouns for variables, verbs for functions.
• Use spaces in between definitions.
• camelCase all variable names, including acronyms.
• For logicals, explicitly write out TRUE and FALSE, instead of using T and F.