Programming languages for biologists

OP here. Let's say I need to look for specific SNPs in a genome, would I use python or R?

Ook!
github.com/leachim6/hello-world/blob/master/o/ook.ok

Probably depends who or what you are working with doesnt it? Its not likely you are going to create something entirely from scratch for this.

Hi folks, are there any good books/lectures to learn R for statistics? I have been using SPSS for quite some time now but would like to switch to R. Thank you in advance!

Neko Programming Language!!!!

:3333333333

High level *Pounce*
SUCH JOY!
*PAWS for dramatic effect*
Many such cases!!!!!!!

en.wikipedia.org/wiki/Neko_(programming_language)

Nya!
Nya!
Nya!

:3

It depends on what discipline of biology you are going into.

If you want to get into genetics and genome sequencing, go Java.

Anything else like health informatics and other non genetics areas go Python.
This is based on how my college does their programs.

Im in python/informatics

python. ignore the R faggots, it will be dead within 10 years.

The problem for R is that Python does everything R does, but also a gazillion things more.

>Which programming language do biologists learn
They don't apparently:
www.popularmechanics.com/science/amp22577/genetics-papers-excel-errors/

Why?

Python.
Obviously not a language, but check out biolinux.

Holy SHIT DAT ROLL!

May I suggest three courses?
ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-00sc-introduction-to-computer-science-and-programming-spring-2011/
ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-0001-introduction-to-computer-science-and-programming-in-python-fall-2016/index.htm
ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-0002-introduction-to-computational-thinking-and-data-science-fall-2016/
I am absolutely certain that they are what you are looking for

>ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-0002-introduction-to-computational-thinking-and-data-science-fall-2016/
Thank you user these seems useful

Python and R, occasionally MATLAB. Once or twice I've pulled Perl off the shelf but Python's taken its role for me.

Neither, you'd use off the shelf tools like sam/bcftools or GATK.

JavaScript is the standard approach

>The problem for R is that Python does everything R does, but also a gazillion things more.
That isn't quite the positive you think it is. R has a specialized focus, yes, but it also means it's tailored for its specialization. R has native data structures and convenience functions that either don't exist in base Python or are harder to work with.

If I want to add a new column to a data frame and populate every row with a single initial value it's as easy as
varName$newCol

sci is a blue board but 18+ still please

R has more highly specialized tools for specific subfields of biology. Sure, expensive, high-throughput genome assembly is not done in R, but if you need a specific statistical test to deal with sparse dataframes, R is a pretty good bet.

Tibshirani's Elements of Statistical Learning and Introduction to Statistical Learning are both easy to obtain, and provide some intro to statistics with R. It will not make you a good R programer, but it will give you a pretty good understanding of how these statistical methods work.

I think that would make you a good R programmer actually. R sucks as a general purpose computing language, but if you approach it as an analysis environment like a statistician does, you're really going to get the most out of your experience.

what do I do if I have 0 knowledge of programming?
I'm trying to understand this
youtube.com/watch?v=32o0DnuRjfg

but it doesn't help at all

They're both useful. Python is a general purpose kind of thing, you can use it for almost anything. R does statistics and graphs a lot more easily, but there's a lot of overlap. R is really good at making 'publication-ready' graphs and tables, too.

They're also conceptually similar enough that if you know one you'll pick up the other pretty quickly, too.

You take a programming course and git gud. An entry level course gets you pretty far pretty quick.

python for libraries/numpy
R for stats
whatever your PI/peers/lab head uses
whatever language the most commonly used tools for your field was written in (usually the above 2, could be something else)
c/c++/rust if you actually have to care about how the computer works (if you have to ask the answer is almost certainly no)

this answer applies to every experimental field in science

>var
its fuckin javascript.

>en.wikipedia.org/wiki/Neko_(programming_language)

You may say "Javascript".
But consider the following...

NYA! :3

I used R for some ecology related things, like population growth modeling and predator prey modeling.

Max Planck?