Index

Shawn T. O’Neil

Index

Symbols | A | B | C | D | E | F | G | H | I | J | K | L
M | N | O| P | Q | R | S | T | U | V | W | X | Z

Symbols

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), [1]

B

C

c() (R function)

call tree

calledprocesserror (error)

categorical data (R)

cbind() (R function), [1]

cd (command)

Central Processing Unit

CPU

character (R)

character classes (regular expressions), [1]

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), [1]

copy-on-write

cp (program)

CPU

Central Processing Unit

CRAN

comprehensive R archive network

cut() (R function)

CyVerse

Atmosphere

D

data frame (R), [1]

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), [1]

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, [1]

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, [1]
defaults
diamonds dataset
discrete data
facet
facet-wrap()
facetting
fill
geom
geom-histogram()
geom-point()
ggsave()

grammar of graphics
layer
layer()
mapping
position
scale, [1], [2]
scale limit
scale transformation
shape
size
stat
theme, [1]
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), [1], [2]

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, [1]

ioerror (error)

iPython notebook

is.na() (R function)

iterable (Python)

iterative development, [1]

J

join (program)

join() (Python method)

K

kernel
keyerror (error)

kill (program)

L

M

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, [1]

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), [1]

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), [1]

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), [1], [2]

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), [1], [2]

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), [1]

fingerprint

stable (sort option)

stage (git)

standard error

standard input, [1], [2]

(R)

standard output, [1]

(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, [1]

swissprot

trembl, uniprot

syntactic sugar, [1]

syntaxerror (error)

T

t.test() (R function)

theme

ggplot2 (R), [1]

tidy data (R)

tidyr (R package)

title

ggplot2 (R)

top (program)

trembl

uniprot swissprot

tuple (Python)

type() (Python function)

typeerror (error), [1], [2], [3]

U

uname (program)

uncompress (program)

uniprot

swissprot trembl

uniq (program)

unique (sort option)

unique() (R function)

unit test, [1]

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, [1]
with (Python keyword)
write.csv() (R function)
write.table() (R function)

X

xrange() (Python function)

Z

zip (program)

License

Icon for the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

A Primer for Computational Biology Copyright © 2019 by Shawn T. O'Neil is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except where otherwise noted.

Symbols

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

Q

R

S

T

U

V

W

X

Z

License

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