Forum:Best programming language for bioinformatics - R Language
Entering edit mode
2.6 years ago
Novogene ▴ 360

Hi everyone,

R language vs Python: Which is the most necessary programming language for a bioinformatician?

I am new to bioinformatics and here is some information for me to get insight into the R programing language. I’m happy to share with you. In my mind, I think the R language is the most suitable language for BI analysis. What do you think?

What is R language?

R is an open-source language for statistical analysis and graphics. The language has been used in a mass of scenarios such as data mining, machine learning, and bioinformatics studies. The package contains a wide range of statistical tests which includes parametric and non-parametric tests for hypothesis testing. Like other languages, it has conditional statements, loops and data structures. R also provides a way to visualize the data and analysis by converting them into plots.

Advantages of R language over other analysis languages

R can handle large data with a large number of columns and rows without compromising the data. In one of the news published by BBC due to restriction of columns and rows in Microsoft excel, Covid-19 data of around 16,000 patients were lost. Due to this loss of data, the number of false negatives increases. This may result in the spread of Covid-19 since those false-negative patients or patients with possible Covid-19 infection can come in contact with other people. This issue can be easily avoided by using R instead of excel where the limit of data is very large as compared to MS Excel.

Application scenarios of the R language in bioinformatics

In life sciences especially in bioinformatics R has been used frequently. Many data analysis algorithms or methods are available in R which was developed by scientific researchers all around the globe. Simple hypothesis tests, like t-test can be used to find the difference in sample data or complex field data can be analyzed using ANOVA which will give the p-value along with other statistics. In biological science co-expression networks between genes using their expression can reveal many interactions pathways which can give insight into the function of genes altogether. In such cases, correlation networks or weighted correlation networks are very helpful. These networks and co-expression can easily be drawn using R. Apart from simple analyses R can be used for NGS analyses. Few of examples include analysis of RNA-Seq, ChIP-Seq, Wole Genome Bisulfite Sequencing, small RNA-seq and many more. Using the Bioconductor package of R all these analyses can be done on a local machine.

Since I am in lack of information about Python, if you think the Python language is also useful for BI analysis, welcome to leave different opinions.

Source of the Blog:

programming R • 4.0k views
Entering edit mode
2.6 years ago
ATpoint 77k

Lets use this thread to make a curated list of all biostars posts discussing choice of programming languages in bioinformatics. Links are sorted by ID, hence by date.

==> What Programming Language Is Best To Learn For Getting Into Web-Based Bioinformatics?

==> Perl Or Python For Comparative Genomics?

==> Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?

==> Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.

==> Csharp For Programming In Bioinformatics

==> Picking A Programming Language And Where To Begin

==> Esoteric Programming Languages

==> C And Fortran Programming Language

==> Beginners resources for biologists to learn Perl applications

==> In Writing Biomedical Applications, Which Disadvantages Of R/Advantages Of Python Made You Switch From R To Python?

==> Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]

==> How To Initiate Learning Perl?

==> Programming Language In Bioinformatics

==> Will Python Take The Place Of R?

==> Anyone Use R For Their Bioinformatics Work?

==> What is the best programming language for NGS data analysis pipeline development?

==> I have to learn another language, but which one?

==> Programming languages for Bioinformatics

==> Learn perl or python for bioinformatics?

==> Manipulating/Extracting Data and Developing Methods - Language Choice

==> Best programming language for pathways and genomics?

==> Java or C++ (which side should I choose)

==> What is the most popular programming language used in bioinformatics?

==> Why bioinformaticians need to know programming languages?

==> Yet Another Programming Language

==> R or python, which one do you prefer in analysing scRNAseq datasets?

==> Python or R

==> Why learn programming in bioinformatics?

==> On the usage of Golang

==> is fortran still used in bioinformatics?

==> Which programming langauge shall I start as a beginner in Bioinformatics

==> which is better for rna-seq analysis? R or python?

==> Programming language to know when using bioinformatic tools such REPET

==> Rust or C++, what to learn after Go for high-performance bioinformatics tools?

==> In 2022 is Perl and Ruby programming languages still useful for bioinformatics?

==> Languages for Bioinformatics

last updated: 10th March 2023


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