Bfx tools

Learning Flavors of Unix and Command-line

UNIX is an operating system around in the 60s and broadly refers to a set of programs that all work the same way at the command-line.  They have the same feel. They have the same philosophy of design.  Ok, its a specific operating system owned by AT&T, however, these days it refers to a program that all follow a common framework. There are many types of Unix – MacOSX, Linux, and Solaris where each of those is essentially different sets of codes owned by different companies or groups to get the common Unix common framework.  MacOSX is owned and developed by Apple.  Solaris is owned by Sun and Oracle.  Linux is open-source and built from a community led by Linus Torvalds, and was meant to work on x86 PCs.  The x86 refers to a type of CPU architecture used across most personal computers today (both Mac and PC).   If I log into a Unix machine in 1980, 1990, 2000, 2010, 2017 – it will often feel and work the same.

• Kenneth Bradnam’s Command line Bootcamp (http://rik.smith-unna.com/command_line_bootcamp). Free one-page resource.
• Lynda.com
  • Various modules dependent on need
• Code Academy (https://www.codecademy.com/). An excellent resource for learning without an account.  Evaluated resources include Learn the Command-line, Website building, and Git. Can be tested for free, or utilizes a $19.95/mo fee
• Ryan’s tutorial (https://ryanstutorials.net/bash-scripting-tutorial/).  Quick and easy w/ good instruction.

R

R is a scripting language enabled and expanded by RStudio. There is the base environment and the R-Studio environment which enables a graphical user interface (GUI) for editing and building reproducible analysis.

• Introduction to R by Thomas Girke.(https://girke.bioinformatics.ucr.edu/manuals/mydoc/mydoc_Rbasics_1.html)
• R & Bioconductor Manual by Thomas Girke UC Riverside (http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual)
• Little Book of R for Bioinformatics (https://a-little-book-of-r-for-bioinformatics.readthedocs.io/).  Free excellent book for pure R.
• DataCamp (https://www.datacamp.com/courses/free-introduction-to-r).  Introductory tool for learning R.  First few chapters are free, though it costs typically $25 per month
• R Basics Cheatsheet. Simple 1 page cheatsheet for basic R functions
• R Importing Data Cheatsheets. Simple 1 page cheatsheet for importing data into R.
• Transforming and manipulating data. Simple cheatsheets for manipulating data with dplyr.
• Top 50 ggplot2 Visualizations. (http://r-statistics.co/Top50-Ggplot2-Visualizations-MasterList-R-Code.html)
• FreeCodeCamp (2hr). Popular R video for learning R.
• Lynda.com. Free for USC faculty , staff and students.
  • Learning R (2hr 51min)
  • R statistics (5h 59m)
  • R for Data Sience (7h 16m)
  • Data Wranging in R (4 h 12 m
  • Data Visualization in R with ggplot2 (2hr 27