Question: how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
0
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)

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
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.

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.

1

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