Programming for Biologists: R, Python and What Else?

[imccafey]

With computational biology and bioinformatics being quite in demand nowadays, is there any other programming language that would come in handy apart from R and Python?

 

[rb32]

Hi imccafey,

They are definitely the two key languages, maybe Matlab as a third. Past basic Python and R I would focus on particular frameworks, such as numpy, scipy, sklearn, scikit-bio. Those frameworks have huge amounts of depth and power.

Good luck!

 

[KylerStern]

Ive heard some people using SPSS, but im not familiar with it myself. The people ive talked to say that everything you need to know can be done with R or Python

 

[rb32]

I would class SPSS as more of a sophisticated statistical tool than a programming language. On that front there is also SAS. SPSS has its strengths, but Python and R are much more flexible.

 

[thetrustedzone]

Python only is enough for that unless you have a reason for not using it.

 

[imccafey]

Hi imccafey,

They are definitely the two key languages, maybe Matlab as a third. Past basic Python and R I would focus on particular frameworks, such as numpy, scipy, sklearn, scikit-bio. Those frameworks have huge amounts of depth and power.

Good luck!

Thank you so much for your suggestions!

 

[imccafey]

Ive heard some people using SPSS, but im not familiar with it myself. The people ive talked to say that everything you need to know can be done with R or Python

I started learning SPSS (from what it looks like, it's somewhat a shortcut data analysis tool). Learning how to use it to compare its differences with Graphpad Prism. Let's see how it goes.

 

[imccafey]

I would class SPSS as more of a sophisticated statistical tool than a programming language. On that front there is also SAS. SPSS has its strengths, but Python and R are much more flexible.

I've reached until dictionaries in python and I kind of like it so far. With R, I've learned the use of vectors and some basic plots. Still a long long way to go.

What I generally have trouble with is thinking about a big picture. Like how do I bring all the stuff I learn altogether? And how do I apply the knowledge in real life cases. I tried a couple of exercises in codewars and well, hit the floor face first

 

[rb32]

I've reached until dictionaries in python and I kind of like it so far. With R, I've learned the use of vectors and some basic plots. Still a long long way to go.

What I generally have trouble with is thinking about a big picture. Like how do I bring all the stuff I learn altogether? And how do I apply the knowledge in real life cases. I tried a couple of exercises in codewars and well, hit the floor face first

In parallel with learning the basics, I would try some applied tutorials such as:
https://www.dataquest.io/blog/sci-kit-learn-tutorial/