Resources

Notes on programming, bioinformatics, and other technical subjects.

Languages

• C++
• Python
• R
• MATLAB
• LaTeX

Programming environments and software engineering tools

• Linux
• Visual Studio Code
• Stanford Computing Resources
• Git
• SSH

Bioinformatics

• General bioinformatics resources
• Nomenclature
• File types
• Common Databases
• Library complexity modeling
• Analyses
  • Gene expression analysis
  • Deconvolution
  • ChIP-seq
• Programs
  • HOMER
  • HTSlib, including samtools and bcftools
  • kallisto/sleuth
  • MEME
  • Pipeline tools, such as snakemake
  • Genome browsers, such as IGV
  • Mass spectrometry software, file formats, and databases
  • Other tools, including online services

Experimental biology

• Microscopy

Mathematics and statistics

• Multiple hypothesis testing
• Expecation maximization (EM) algorithm

Other

• Miscellaneous