Index

Symbols

• ! (R operator)
• ! (shebang)
• $-syntax (R),
• %>% (“not a pipe” R operator)
• %in% (R operator)
• & (R operator)
• * (shell wildcard)
• . (in R)
• . and .. (virtual directories)
• … (R),
• .bash-login (file)
• .bashrc (file)
• .git (directory)
• .gitignore (file)
• / (root directory)
• 2> redirect (bash)
• <- (R assignment)
• > or >> redirect
• ? (shell wildcard)
• [[]]-syntax (R)
• [] (Python)
  • slice syntax (Python)
• []-syntax (R)
• `+`() (as R function)
• | (R operator)
• | redirect
  • pipe,

A

• absolute path
  • path
• aes()
  • ggplot2 (R)
• algorithms
• alpha
  • ggplot2 (R)
• annotation
  • ggplot2 (R)
• ANOVA model (R)
• any() and all() (R functions)
• API
  • application programming interface
• append() (to a Python list)
• application programming interface
  • API
• apply() (R function)
• argv (Python list)
• arrays (R)
• as.character() (R function)
• as.numeric() (R function)
• assembly
  • bytecode
• assert (Python)
• Atmosphere
  • CyVerse
• attach() (R function)
• attributes (R)
• AVL tree (data structure)
• awk (program),

B

• back-reference (regular expression)
• bash script
  • command-line argument
  • environment variable
  • if-statement
  • script
• big-O notation
  • order notation
• binary search tree (data structure)
• BioConductor (R)
• bioinformatics
• BioPython
• BLAST: Basic Local Alignment Search Tool
• block (Python)
  • (R)
• BLOSUM (BLAST scoring matrix)
• boolean (Python)
• boolean operators (Python)
• boxplot()
  • ggplot2 (R)
• BSD Unix (history)
• bubblesort (algorithm)
• bunzip2 (program)
• bytecode
  • assembly

C

• c() (R function)
• call tree
• calledprocesserror (error)
• categorical data (R)
• cbind() (R function),
• cd (command)
• Central Processing Unit
  • CPU
• character (R)
• character classes (regular expressions),
• chgrp (program)
• chmod (program)
• chown (program)
• class (Python)
• class attribute (R)
• class of vector (R)
• class() (R function)
• client
• clone (git installation)
• colnames() (R function)
• color
  • ggplot2 (R)
• column (program)
• column-major order
  • row-major order
• command line interface (CLI)
• command prompt
• command-line argument
  • bash script
• command-line arguments (Python)
  • (R)
• comments (Python)
  • (R)
• commit (git)
• comparable objects (Python)
• comparison (R)
• compilation
  • see software installation
• compiled languages
• comprehensive R archive network
  • CRAN
• computational biology
• condition has length > 1 (warning)
• configure (program)
• constructor (Python)
  • (R)
• continuous data
  • ggplot2 (R)
• coordinate
  • ggplot2 (R),
• copy-on-write
• cp (program)
• CPU
  • Central Processing Unit
• CRAN
  • comprehensive R archive network
• cut() (R function)
• CyVerse
  • Atmosphere

D

• data frame (R),
• data structures
• defaults
  • ggplot2 (R)
• delete data frame column
• deleting list elements (R)
• diamonds dataset
  • ggplot2 (R)
• dictionaries (Python)
• diff (git)
• dim() (R function)
• discrete data
  • ggplot2 (R)
• dispatch (R)
• divide and conquer (algorithms/data structures)
• do() (R function)
• docstring (Python)
• documentation (R functions)
• DOS newlines
  • unix newlines
• dplyr (R package)
• du (program)

E

• e-value (BLAST)
• echo (program)
• encapsulation
• env (program),
• environment variable
  • bash script
• escaping special characters
• executable
• exit (program)
  • logout
• export (program)
• external programs (Python)
• extract() (R function)

F

• facet
  • ggplot2 (R)
• facet-wrap()
  • ggplot2 (R)
• facetting
  • ggplot2 (R)
• factorial function
• factors (R)
• FASTA format,
• fasta-stats (program)
• FASTQ format
• Fibonacci function
• file handle (Python)
• filesystem
• fill
  • ggplot2 (R)
• finger (program)
• fingerprint
  • ssh (program)
• float (Python)
• flybase
• for-loop (bash)
  • (Python)
  • (R)
• for-loop speed (R)
• formula (R)
• function (Python)
• function arguments (R)
• functional programming
• functions (R)
• functions as data (R)

G

• garbage collection
• gather() (R function)
• generic functon (R)
• geom
  • ggplot2 (R)
• geom-histogram()
  • ggplot2 (R)
• geom-point()
  • ggplot2 (R)
• getter method
• ggplot2 (R)
  • PDF output
  • aes()
  • alpha
  • annotation
  • boxplot()
  • color
  • continuous data
  • coordinate,
  • defaults
  • diamonds dataset
  • discrete data
  • facet
  • facet-wrap()
  • facetting
  • fill
  • geom
  • geom-histogram()
  • geom-point()
  • ggsave()
  • grammar of graphics
  • layer
  • layer()
  • mapping
  • position
  • scale, ,
  • scale limit
  • scale transformation
  • shape
  • size
  • stat
  • theme,
  • title
• ggsave()
  • ggplot2 (R)
• git (program)
• GNU (GNU’s Not Unix)
• gnuplot (program)
• GPL
  • GNU Public License
• grammar of graphics
  • ggplot2 (R)
• graphical user interface (GUI)
• greedy matching (regular expression)
• grep (program), ,
• group-by() (R function)
• grouped data frame (R)
• groups (command)
• gzip (program)

H

• Hard Drive
• hash tables
  • see dictionaries (Python)
• head (program)
• help() (Python function)
  • (R function)
• hidden files
• high scoring pair
  • HSP
• hit (BLAST)
• HMMER (midden markov protein search)
• home directory
• HSP
  • high scoring pair

I

• IDE
  • integrated development environment
• if-statement
  • bash script
• if-statement (awk)
  • (Python)
  • (R)
• immutable
• import (Python)
• in keyword (Python)
• indentationerror (error)
• inheritance (Python)
• installing a program
• instance variable (Python)
• integer (Python)
  • (R)
• integrated development environment
  • IDE
• interactive interpreter (Python)
• interactive programs (Python)
• interpreter,
• ioerror (error)
• iPython notebook
• is.na() (R function)
• iterable (Python)
• iterative development,

J

• join (program)
• join() (Python method)

K

• kernel
• keyerror (error)
• kill (program)

L

• lapply() (R function)
• layer
  • ggplot2 (R)
• layer()
  • ggplot2 (R)
• len() (Python function),
• length() (R function)
• less (program)
• levels (in R factors)
• levels (of factors, R)
• lexicographic order
• library (R)
• linked list (data structure)
• Linux (history)
• list (Python)
  • (R)
• list comprehensions (Python)
• list() (Python function)
• lists and strings (Python)
  • strings and lists (Python)
• load() (R function)
• local variable,
  • (R)
• logical (R)
• logical selection (R)
• logout
  • exit (program)
• longer object length is not a multiple of shorter (warning)
• ls (program)

M

• make (program)
• makefile
• man (program)
• mapping
  • ggplot2 (R)
• markdown (in RStudio)
• matrices (R)
• mean() (R function)
• median() (R function)
• merge() (R function)
• mergesort (algorithm)
• method (Python)
  • (R)
• method chaining
• microarray
• mkdir (program)
• module
  • (Python)
• modulus (Python)
  • (R)
• monte-carlo method
• mounting (in a filesystem)
• multiple test correction (R)
• muscle (program)
• mutable
  • (Python)
• mv (program)

N

• NA (R)
• na.rm (R)
• named list (R)
• named vectors (R)
• nameerror (error)
• names() (R function)
• namespace
• NaN (R)
• nano (program)
• NAs induced by conversion (warning)
• NAs introduced by coercion (warning)
• ncol() (R function)
• network connection
• newline
• newlines (Python)
• non-greedy (regular expressions)
  • reluctant (regular expressions)
• nrow() (R function)
• numeric (R)

O

• object (Python)
• object not found (error)
• omitting directory (error)
• order notation
  • big-O notation
• order() (R function)

P

• p.adjust() (R function)
• package (Python)
  • (R)
• PAM (BLAST scoring matrix)
• parameters (Python functions)
• pass by value vs. reference
• pass-the-buck (data structures)
• passwd (program)
• path
  • absolute path
  • relative path
• PATH (environment variable)
• PDF output
  • ggplot2 (R)
• permission denied (error)
• permissions
• pipe
  • | redirect,
• plot() (R function)
• polymorphism (Python)
  • (R)
• position
  • ggplot2 (R)
• POSIX
• pre-allocation (R)
• prefix
  • see configure (program)
• present working directory
  • PWD
• principle of command-query separation
• process substitution (bash)
• ps (program)
• pseudocode
• pure function
• Putty.exe (program)
• PWD
  • present working directory
• PWD (R)
  • present working directory (R)

Q

• quantile() (R function)
• quicksort (algorithm)
• Quine

R

• RAM
  • Random Access Memory
• random module (Python)
• Random Access Memory
  • RAM
• random data (R)
• range() (Python function)
• raw string (Python)
• rbind() (R function)
• re-running commands
• read.csv() (R function)
• read.table() (R function)
• recursion
• red-black tree (data structure)
• reference classes (R)
• regular expression
  • (R),
• relative path
  • path
• reluctant (regular expressions)
  • non-greedy (regular expressions)
• reordering factors (R)
• rep() (R function)
• replace() (Python method)
• repository (git)
• results are not data frames (error)
• rev() (R function)
• reverse complement
• reverse() (Python function)
• rexp() (R function)
• RGB color system
• rm (program)
• RNA-seq
• rnorm() (R function)
• rounding errors (Python)
  • (R)
• row-major order
  • column-major order
• Rscript (program)
• RStudio
• rule 1 (functions),
• runif() (R function)

S

• S3 object system (R)
• S4 object system (R)
• sample() (R function)
• sanity checking with uniq
• sapply() (R function)
• save() (R function)
• scale
  • ggplot2 (R), ,
• scale limit
  • ggplot2 (R)
• scale transformation
  • ggplot2 (R)
• scope (of a variable)
  • (R variables)
• scp (program)
• script
  • bash script
• script (Python)
• sd() (R function)
• search() (Python function)
• sed (program), ,
• selective replacement (R)
• self (Python)
• separate() (R function)
• seq() (R function)
• server
• setenv (program)
• setter method
• setwd() (R function)
• SFTP (secure file transfer)
• shadowing (local variables)
• shape
  • ggplot2 (R)
• shell
• shell alternatives (bash, tcsh)
• shell command
• shell variable
• sickle (program)
• side-effect-free function
• simulation (Python)
• size
  • ggplot2 (R)
• slice (Python)
• slice syntax (Python)
  • [] (Python)
• software installation (source and binary)
• sort (program)
• sort() (R function)
  • see order() (R function)
• sorting (algorithms)
• spaghetti code
• split() (Python function)
  • (Python method)
• split-apply-combine (R)
• splitting columns (R)
• spread() (R function)
• SQL
  • structured query language
• ssh (program),
  • fingerprint
• stable (sort option)
• stage (git)
• standard error
• standard input, ,
  • (R)
• standard output,
  • (R)
• stat
  • ggplot2 (R)
• str() (R function)
• str-c() (R function)
• str-detect() (R function)
• strategy (programming)
• string (Python)
• string concatenation (Python)
• stringr (R package)
• strings and lists (Python)
  • lists and strings (Python)
• stringsAsFactors (R)
• structured query language
  • SQL
• subn() (Python function)
• subprocess (Python)
• subroutine
• subset() (R function)
• sum() (Python function)
  • (R function)
• summarize() (R function)
• swapping,
• swissprot
  • trembl, uniprot
• syntactic sugar,
• syntaxerror (error)

T

• t.test() (R function)
• tab-completion
• tail (program)
• tar (program)
• telnet (program)
• theme
  • ggplot2 (R),
• tidy data (R)
• tidyr (R package)
• title
  • ggplot2 (R)
• top (program)
• trembl
  • uniprot swissprot
• tuple (Python)
• type() (Python function)
• typeerror (error), , ,

U

• uname (program)
• uncompress (program)
• uniprot
  • swissprot trembl
• uniq (program)
• unique (sort option)
• unique() (R function)
• unit test,
• Unix (history)
• unix newlines
  • DOS newlines
• unlist() (R function)
• usage line (for software)
• UseMethod() (R function)

V

• valueerror (error)
• variable (Python)
• VCF format
• vector recycling (R)
• vectorized operations (R)
• vectors (R)
• version (git)
• version control

W

• wc (program)
• wget (program)
• which (program)
• while-loop (Python)
  • (R)
• whitespace,
• with (Python keyword)
• write.csv() (R function)
• write.table() (R function)

X

• xrange() (Python function)

Z

• zip (program)