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How to choose the best R package for analysing gene expression?

3 years ago in Bioinformatics and Computational Biology , Differential Gene Expression By Anjum

Bioinformatics Differential Gene

Hello, I am performing research in Biometrics and Computational Biology where I have to identify genes expressed from a single family and are differentially expressed. I am using GEO datasets but I am confused which R package will be the most suitable for the analysis.

If anyone can help me decide, it would be greatly appreciated.

Thank you very much in advance.

All Answers (3 Answers In All)

By Jayanti Patil Answered 3 years ago

I was trying to search about the types of R packages as well. Thanks for asking this question, I will be looking forward to this discussion. All the best dear.

Replied 3 years ago

By Anjum

Hi Jayanti, I am glad you are finding this discussion helpful. I hope we both get our answers.

By Rafael Answered 3 years ago

Hi Anjum, as for the method many researchers have been using the RNA-seq for the gene expression analysis. But when it comes to software tools, there are a few emerging softwares like Ball Gown, StringTie, and HISAT which can be used to measure, compare, and analyse the gene expression. I am attaching a few links below and I hope it will help you. https://www.nature.com/articles/nprot.2016.095 https://davetang.org/muse/2017/10/25/getting-started-hisat-stringtie-ballgown/ https://rpubs.com/selveyad/ballgown_tutorial

Replied 3 years ago

By Anjum

Hello Rafael, thank you so much for your reply and these links. I will make sure to check these out.

By Mani Answered 3 years ago

There’s no one or two methods for the analysis and it depends on the result. The one you find the closest to your expected result of the research hypothesis becomes the right method of analysis for your research. I don’t know if it will help or not, but you can go through the workflow I am attaching below. Maybe it helps. https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html In case you still don't get the hold of the answer or how to differentiate the gene expression of various genes, then do contact an expert who can help. Best wishes for your research work.

Replied 3 years ago

By Anjum

Hi Mani, thank you for the link. If you don’t mind, can you also please suggest an expert who can help as well, just in case? I don’t trust sites directly as it is hard to see which is authentic and which is not.

Replied 3 years ago

By Mani

As such I haven’t taken direct help from experts as well but my cousin did. There is a site by the name Chanakya Research, you can search for them directly. You can consult with them first and see for yourself if they can help. My cousin told me they were good.

Replied 3 years ago

By Anjum

Oh okay, thank you so much Mani.

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