README.md

PughLabReadme

Documentation of best practices, coding tips, and ongoing projects developed by the Pugh Lab

Labels (in addition to your own custom ones)

• Cancer genome variant:
  • copy-number
  • fusion
  • SNP
  • SNV
  • structural-variant
  • mutation-signature
• Topics:
  • immunogenomics
  • Bulk RNA-seq
  • single-cell
  • cell-free-dna
  • epigenetics
  • methylation
  • minimal-residual-disease
• Type:
  • wrapper
  • pipeline
  • tool
  • package
  • docker

Documentation

• General guideline:

  • ALWAYS comment your code
  • Document all functions!!
  • Add README document when there’s other people who will be using your tool
  • For R, use documentation within code and easily port to markdown with Roxygen: http://r-pkgs.had.co.nz/man.html

• Google Python style guide:

  • https://google.github.io/styleguide/pyguide.html

• Google R style guide:

  • https://google.github.io/styleguide/Rguide.xml