Question: What kind of R Project I can do related to gene expression analysis or protein comparison
0
gravatar for koushikayaluri
10 months ago by
koushikayaluri20 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 • 341 views
ADD COMMENTlink modified 10 months ago by JC9.1k • written 10 months ago by koushikayaluri20
2

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 REPLYlink written 10 months ago by JC9.1k

Thank You will look into it.

ADD REPLYlink written 10 months ago by koushikayaluri20
0
gravatar for Giovanni.madrigal12
10 months ago by
Giovanni.madrigal12120 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 COMMENTlink written 10 months ago by Giovanni.madrigal12120

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 REPLYlink modified 10 months ago • written 10 months ago by Friederike5.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1312 users visited in the last hour