NVIDIA-Genomics-Research / AtacWorks

Deep learning based processing of Atac-seq data
https://clara-parabricks.github.io/AtacWorks/
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Jupyter notebooks for tutorials #167

Closed ntadimeti closed 4 years ago

ntadimeti commented 4 years ago

Added jupyter notebooks for tutorials

ntadimeti commented 4 years ago

todo: Add CI support to run them. Will be addressed as a separate PR

ntadimeti commented 4 years ago

@avantikalal cool! Is there a way to not save the output in the jupyter file ? Is it important/informative to save the outputs ?

avantikalal commented 4 years ago

@ntadimeti for a tutorial, I think it's much better to have the outputs so the user knows what to expect.

ntadimeti commented 4 years ago

@avantikalal fixed all errors. Could you take a look ?

avantikalal commented 4 years ago

@ntadimeti I went to your branch, the images are not displayed in either tutorial notebook.

avantikalal commented 4 years ago

I also think that we need some explanation for readers who are not familiar with running bash commands from a Jupyter notebook. People who haven't done this before may not understand what is going on. We should explain that we are running the commands from within a python notebook, but all these commands can be run from the command line without the ! in front. And for os.chdir we should say that we are entering the newly created directory.

avantikalal commented 4 years ago

Otherwise this looks good

ntadimeti commented 4 years ago

fixed the paths to the images and the tutorial links. @avantikalal --can you take a look again ?

avantikalal commented 4 years ago

This looks good!