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Programming language for Computational Biology

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
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updated by Ram Ram • written by shiningstarbzu • shiningstarbzu

2 answers

Suggest Julia for computational biology.

See OpenGene as an example

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updated by Ram Ram • written by chen chen

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.

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updated by Ram Ram • written by cbio cbio

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).

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updated by Ram Ram • written by Chris Fields Chris Fields

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

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written by ATpoint ATpoint

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.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

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

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written by shiningstarbzu • shiningstarbzu

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

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written by Devon Ryan Devon Ryan

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.

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written by romain.lannes romain.lannes

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

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updated by Ram Ram • written by Ben Ben

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