Question: Programming language for Computational Biology
0
gravatar for shiningstarbzu
2.5 years ago by
shiningstarbzu10 wrote:

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.

genome • 1.1k views
ADD COMMENTlink modified 2.5 years ago by chen1.7k • written 2.5 years ago by shiningstarbzu10
3
gravatar for chen
2.5 years ago by
chen1.7k
OpenGene
chen1.7k wrote:

Suggest Julia for computational biology.

See OpenGene as an example

ADD COMMENTlink written 2.5 years ago by chen1.7k
1

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).

ADD REPLYlink written 2.5 years ago by Chris Fields1.9k

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

ADD REPLYlink written 4 months ago by ATpoint6.6k

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. 

ADD REPLYlink written 2.5 years ago by cbio370
2
gravatar for Devon Ryan
2.5 years ago by
Devon Ryan82k
Freiburg, Germany
Devon Ryan82k wrote:

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 (https://github.com/bxlab/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.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Devon Ryan82k

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

ADD REPLYlink written 2.5 years ago by shiningstarbzu10

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

ADD REPLYlink written 2.5 years ago by shiningstarbzu10
2

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

ADD REPLYlink written 2.5 years ago by Devon Ryan82k
1

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.

ADD REPLYlink written 2.5 years ago by romain.lannes80
1

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

ADD REPLYlink written 2.5 years ago by Ben2.0k
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