Programming language for Computational Biology

Question

[shiningstarbzu]

Hello Dears,

I am new user in the field of computational biology and want to handle Hi-C(3C) data. For this purpose which programming language is best and easy to learn so that can handle it easily.

Thanks for your time.

Answer 1

[chen]

Suggest Julia for computational biology.

See OpenGene as an example

[Chris Fields]

I like Julia but as a first language for someone in bioinformatics to learn I don't think it's the best pick. These days it would be python and/or R (and I say that as a perl developer).

[ATpoint]

Agreed. I would start with R simply to be able to make use of the Bioconductor ressources.

[cbio]

I'd be interested in where you think someone could go to learn such a young language? I've always been pretty interested in taking in another language to compliment R, but have always just banked on eventually learning Python.

Answer 2

[Devon Ryan]

Do you need to write programs for it or just analyse it? There are already some tools for the latter (typically in python), so don't reinvent the wheel unless you really need to.

BTW, examples of existing program would be HiCExplorer (it's by a colleague of mine and hasn't been fully released yet) or HiFive from James Taylors group. Those happen to both be written in python, though I wouldn't be surprised if others are a mixture of python and R.

[shiningstarbzu]

@Devon Ryan Thanks. I just want to analyse the data...

[shiningstarbzu]

Because before i never used any programming language so i want to learn it for my future. Your suggestion is about "Python"?

[Devon Ryan]

For this sort of task python will probably be the most useful.

[romain.lannes]

python is designed to be easy to write and easy to read. It come with a lot of library and a huge community. If you want to learn programing is the langague of choice.

[Ben]

Hiclib is a well-establshed python library for Hi-C processing. For downstream analysis and visualisation you could try juicebox.