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

! (R operator)
#! (shebang)
$-syntax (R), [1]
%>% (“not a pipe” R operator)
%in% (R operator)
& (R operator)
* (shell wildcard)
. (in R)
. and .. (virtual directories)
… (R), [1]
.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, [1]

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

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), [1]
cd (command)
Central Processing Unit
CPU
character (R)
character classes (regular expressions), [1]
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), [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

lapply() (R function)
layer
ggplot2 (R)
layer()
ggplot2 (R)
len() (Python function), [1]
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, [1]
(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, [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)
tab-completion
tail (program)
tar (program)
telnet (program)
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)