Bioinformatics information

A resource for ARU students who wish to know more about bioinformatics, computing, and programming.

Directory structure

• general contains an overview of basic terminal practice
  • the filesystem overview and navigation: ls, cd, pwd
  • help: man, -h/--help
  • filesystem: mkdir, cp, mv, rm, hidden files
  • viewing: head, more/less, wc
  • pipes and redirection: |, >, >>
  • file manipulation: awk, sed, cut, sort, uniq, grep
  • fetching data: curl, tar, gzip, unzip, gunzip
  • the shell environment: aliases, $PATH
  • permissions: chmod
• R topics in R
  • statistics
    • descriptive stats: means, sd's, table, histogram
    • describe data: error and confidence intervals
    • categorical x categorical: chi squared analysis
    • numerical x categorical: t test & anova
    • numerical x numerical: correlation, regression analysis, lm
    • meta-analysis in R
    • ANCOVA?
    • glm
  • general programming
    • variables, data types, classes
    • reading, indexing, and writing data frames
    • functional programming, writing and applying functions
    • string manipulation
    • plotting - base
    • the tidyverse
      • dplyr, tidyr, ggplot2
• scripting will contain help in making scripts in BASH, R, python
  • running files: ./
• git
  • basic commands