how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
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@thindmarsmission-17577
Last seen 3.7 years ago

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:

edger clustering visualization • 562 views
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@james-w-macdonald-5106
Last seen 3 hours ago
United States

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.

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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.
 

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

 

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