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bgruening / galaxy-ipython

:microscope::books: IPython Integration into Galaxy
MIT License
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Lack of example history #11

Closed hexylena closed 9 years ago

hexylena commented 10 years ago

In order to showcase the full powers of our package we should build an example history that users can view and import (dunno how that'd work across galaxies).

It should have some example tabular/sam datasets and then we should have a couple notebooks for each of the different major graphics packages we have.

jmchilton commented 9 years ago

So after many false starts finally made some progress on my cummeRbund idea (nbviewer.ipython.org/github/jmchilton/ipython_notebooks/blob/master/cummerbund_galaxy_1.ipynb), but made it made a guy on Twitter really mad me http://imgur.com/AjUUScj for reasons I am not smart enough to understand. I may have to put the FASTQ files down and go back to text filtering tools.

hexylena commented 9 years ago

Okay, the notebook looks excellent for what it's worth. ggplot2 is just so pretty...

I, likewise, am not really up on rna-seq data analysis, so can't comment on his complaints. Perhaps someone will be so kind as to make a PR....

Otherwise looks great! With the planned language selection interface I imagine we'll have the option to "load an example notebook", so we'll use this. :-D

Thanks so much for putting one together! I'll probably create an RStudio duplicate, whenever I fix the one remaining bug there.

On October 23, 2014 1:25:50 AM GMT+00:00, John Chilton notifications@github.com wrote:

So after many false starts finally made some progress on my cummeRbund idea (nbviewer.ipython.org/github/jmchilton/ipython_notebooks/blob/master/cummerbund_galaxy_1.ipynb), but made it made a guy on Twitter really mad me http://imgur.com/AjUUScj for reasons I am not smart enough to understand. I may have to put the FASTQ files down and go back to text filtering tools.

Reply to this email directly or view it on GitHub: https://github.com/bgruening/galaxy-ipython/issues/11#issuecomment-60180868

Sent from my Android device with K-9 Mail. Please excuse my brevity.

bgruening commented 9 years ago

@jmchilton unfortunately he is correct. I think you need a so called TPM measure https://liorpachter.wordpress.com/tag/tpm/. Not sure if cummeRband is able to calculate this. We can also add d3,js to the notebook if we want to have even more wow :).

This presentation will be earthshaking. I wish it would be recorded!