Computational Biology (Bio 381) Lecture Notes
April D. Makukhov
January 24, 2017

New Project
Directory on Desktop

Tools, global options

-Unclick Insert matching parens/quotes
-Check soft-wrap R source files

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•Plain-text files: 
-simple characters only, can generally open in any computer, 'run the world'. WYSIWYW (what you see is what you want)

•Several languages within them:
1) LaTex - thousands of typesetting commands (we will use when we make slides and when we make equations in R Markdown)
2) Markdown - very simple version of LaTex
3) R Markdown - (many versions of Markdown, like dialects of a language). Will be able to mix in lines of R code and be able to run.

•We will create a plain-text file: Filename.Rmd (R markdown file extension)
•We will "knit" our R markdown file into 1 of 3 possible formats:
	-Filename.html
	-Filename.pdf
	-Filename.docx

R Markdown document:

•yaml: (yet another markdown language) - for the most part we won't mess with it (spacing of it quite important)	
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• Markdown template - we erase this at the beginning and insert our own stuff

•Ctrl (or command), shift, K = "knit"

• Help, Markdown Quick Reference provides text formatting reference info
• Command + alt+ i = insert R-code chunk

Format I like: highlight: pygments, theme: cerulean