IPython & R had a baby…Rpy2 :)

Running R in IPython to run the WGCNA package. See the code below:

…Hopefully this is not the GoPRO Video that shows below:

Awesome, I know!

We also spent the AFTERNOON split into three teams to focus on different areas of analysis: 1) overall transcriptome, 2) DEG homology & consistency, and 3) enrichment analyses

Our group focused on the transcriptome overall; trying to mine taxon specific fields (i.e. bacteria-related only, fungi-related only, echinoderm-related only, etc…). In order to see what areas of the KEGG pathways our transcriptome covers (echinoderm-specific), I joined our 05 swissprot list with the blastnt list and mined for only contigs containing either “urchin”, “star”, or “echino” and then within SQLshare I took out only the swissprot IDs to load into iPATH2. Sadly, there’s still some issue an it wouldn’t run in iPATH2. But I hope to soon have results in a format similar to this…

 

Screen Shot 2014-08-08 at 5.27.01 PM

I will have to tinker with it. Below is my notebook, outlining all the steps taken (besides those steps done in SQLshare).

 

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