Question: how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
0
gravatar for thindmarsmission
13 months ago by
thindmarsmission0 wrote:

Hi!!

I want to plot trends between genes across different conditions from my normalized count matrix (featurecount-EdgeR).

I was using "csCluster" in cummerbund. Now I switched to this pipeline and I am wondering, if similar pacakage or tool is available for plotting those kinds of trends. eg : below image (ref:cummerbund kellis lab)

https://www.google.de/search?q=cummerbund+cscluster&source=lnms&tbm=isch&sa=X&ved=0ahUKEwil_eWVheXdAhUixYUKHSfVBbQQ_AUIDigB&biw=1920&bih=1076#imgrc=5-d88IDIi9WRCM:

ADD COMMENTlink modified 13 months ago by James W. MacDonald51k • written 13 months ago by thindmarsmission0
Answer: how to plot trends for differentialy expressed genes from normalized count matri
2
gravatar for James W. MacDonald
13 months ago by
United States
James W. MacDonald51k wrote:

Those are just regular line plots from ggplot2. There is (literally) a metric ton of questions/answers about doing stuff with ggplot2, which you can easily Google for.

ADD COMMENTlink written 13 months ago by James W. MacDonald51k

Thank you, but for clustering the genes having similar trends throughout, what I can use ? I am new to this field.  sorry for stupid questions.
 

ADD REPLYlink modified 13 months ago • written 13 months ago by thindmarsmission0
1

The csCluster function uses pam (partitioning around medioids) from the cluster package.

 

ADD REPLYlink written 13 months ago by James W. MacDonald51k
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 16.09
Traffic: 169 users visited in the last hour