Closed cgreene closed 8 years ago
@bvoight What do you think about starting with browser-based methods. UCSC (and motifs? didn't notice programming there but might have missed it - @ksiewert ). Then progressing through Unix & ChIP-Seq. Then we could hit R/Python and the modules that use them.
Also - if TAs have any records of what assignments were the most trouble to people based on inference from office hours ( @alexamlie @ksiewert ) that'd be great. Doesn't look like the students provided specifics.
UCSC doesn't use much programming; motifs etc. uses bedtools as the main thing. So, I think the'd need to know some UNIX before they ran with this. -BV
Benjamin F. Voight, Ph.D. Assistant Professor, Departments of Pharmacology and Genetics The University of Pennsylvania - Perelman School of Medicine Tel: (215) 746-8083; Email: bvoight@upenn.edu; Twitter: @bvoight28 https://twitter.com/bvoight28 http://coruscant.itmat.upenn.edu
On Mon, Jun 20, 2016 at 10:41 AM, Casey Greene notifications@github.com wrote:
@bvoight https://github.com/bvoight What do you think about starting with browser-based methods. UCSC (and motifs? didn't notice programming there but might have missed it - @ksiewert https://github.com/ksiewert ). Then progressing through Unix & ChIP-Seq. Then we could hit R/Python and the modules that use them.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/greenelab/GCB535/issues/30#issuecomment-227162160, or mute the thread https://github.com/notifications/unsubscribe/AHQFKwuev7oDI9Yax90bZYcadtEDeDH6ks5qNqZ9gaJpZM4I5thk .
ENCODE ipynbs aren't loading for me right now - I think they might just depend UNIX/Databases but not sure.
The hardest assignments were definitely the the bioconductor ones, so we ended giving them an extra class to do them (11 and 12 I think were the numbers). Are the ENCODE ipynbs loading now? I updated new versions.
@ksiewert : Might be the github interface. I still get failure to load on chrome. Any luck for you?
Yeah, ENCODE 1 isn't working for me on the github interface, but ENCODE 2 is. Let me e-mail you the .ipynb notebook file, and maybe you can try uploading it? Might be a jupyter for linux issue?
I think it's probably just timing out in the rendering. I can clone the repo and see it, so I'm not too worried.
On Wed, Jul 6, 2016 at 3:24 PM ksiewert notifications@github.com wrote:
Yeah, ENCODE 1 isn't working for me on the github interface, but ENCODE 2 is. Let me e-mail you the .ipynb notebook file, and maybe you can try uploading it? Might be a jupyter for linux issue?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/greenelab/GCB535/issues/30#issuecomment-230879441, or mute the thread https://github.com/notifications/unsubscribe/AAhHs2YTn9DNsnAOqejGHOtEA1sGagXoks5qTADogaJpZM4I5thk .
The course has been reorganized to address these concerns. Closed by #59