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Question: What kind of R Project I can do related to gene expression analysis or protein comparison
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gravatar for koushikayaluri
21 months ago by
koushikayaluri • 20
koushikayaluri • 20 wrote:

I am currently learning R and want to do a practical project using R programming language can you please suggest any particular topic/data set I can focus on. I am interested in gene expression analysis.
bioinformatics R • 516 views
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modified 21 months ago by JC ♦ 12k • written 21 months ago by koushikayaluri • 20
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Hi, I edited your post, this is a question, not a tutorial.

Regarding your project, first I will take a look into R-related packages (limma, affy, edgeR, DESeq)

ADD REPLY • link written 21 months ago by JC ♦ 12k

Thank You will look into it.

ADD REPLY • link written 21 months ago by koushikayaluri • 20
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gravatar for Giovanni.madrigal12
21 months ago by
Giovanni.madrigal12 • 170
Giovanni.madrigal12 • 170 wrote:

If you're able to learn some command line to utilize tools like Salmon, DESeq would be a great tool to use. A workflow can be found here.
ADD COMMENT • link written 21 months ago by Giovanni.madrigal12 • 170

If you want to skip the first command-line-based steps, you could start from the read counts using the recount package and their workflow

EDIT: Some background info -- both, Giovanni and me, recommend you dive into comparing the gene expression profiles derived from RNA-seq for multiple samples. That's a classical bioinformatics and R-based analysis called differential gene expression -- you may want to read up on the general details of RNA-seq before you start the analysis so that the results make more sense. Conesa et al., 2016 might be a good starting point.

ADD REPLY • link modified 21 months ago • written 21 months ago by Friederike ♦ 6.5k
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