Cheat sheet for everyday computational analysis

Quick reference cheatsheet for frequently used commands for languages like bash, R, slurm etc.

Bash quick reference

Command	Purpose	Example
~	Your home directory	cd ~
/	Filesystem root and path separator	cd /scratch
pwd	Print working directory	pwd
ls	List files and directories	ls -lh results
cd	Change directory	cd data/raw
cd ..	Move up one directory	cd ..
mkdir -p	Create directory/directories	mkdir -p logs results
head	Show the beginning of a file	head -n 5 file.txt
less	View a file interactively; press q to exit	less file.txt
grep	Search for text in a file	grep "value" file.txt
wc -l	Count lines	wc -l file.txt
curl -L -o	Download URL into a named file	curl -L -o file.txt URL

R quick reference

R basics

Function/operator	Purpose	Example
c()	Combine values into a vector	c(1, 2, 3)
<-	Assignment	x <- 5
read.delim()	Read a tab-delimited file	read.delim("data/raw/file.txt")
str()	Show structure/types of an object	str(df)
dim(), nrow(), ncol()	Dimensions of a data frame	dim(df)
head() / tail()	First/last rows	head(df, 5)
summary()	Quick numeric/factor summary	summary(df$Height)
df$col	Access a column by name	df$Fitness
df[rows, cols]	Subset by position/condition	df[df$Region == "E", ]
table()	Count occurrences	table(df$Population)
tapply() / aggregate()	Grouped summaries	tapply(df$Height, df$Population, mean)
function(...) {}	Define a function	f <- function(x) mean(x, na.rm = TRUE)
for (i in seq)	Loop	for (p in unique(df$Population)) {...}
hist(), boxplot(), plot()	Base R plotting	hist(df$Height)
write.csv()	Save a table	write.csv(x, "results/out.csv")

R for bioinformatics quick reference

Function/package	Purpose	Example
matrix()	Build a genotype matrix	matrix(..., nrow, ncol)
colMeans()	Column-wise means (used for allele freq.)	colMeans(geno) / 2
prcomp()	Principal component analysis	prcomp(geno, scale. = TRUE)
cor.test()	Test correlation between two variables	cor.test(x, y)
lm()	Fit a linear model	lm(y ~ x1 + x2, data = df)
vegan::rda()	Redundancy analysis (multivariate GEA)	rda(Y ~ x1 + x2, data = df)
vcfR::read.vcfR()	Read a real VCF file (beyond this module)	read.vcfR("file.vcf")
adegenet::genind	Genotype container object (beyond this module)	df2genind(...)