Bioinformatics python capstone lesson#608
Bioinformatics python capstone lesson#608rbeagrie wants to merge 12 commits intoswcarpentry:masterfrom
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To be replaced with permutation
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cc @janezd, @BlazZupan |
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What kind of feedback and suggestions are you looking for? Also, what is the audience for the lesson? Presumably they won't all be genomics experts. It seems useful to provide some domain context and explanation for the example. |
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In this case we're assuming they are knowledgeable about genomics, but |
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I think some more explanation about the output of the various commands would help. The output of |
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Typo: "the overlap" -> "they overlap".
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Ah, nice! Here is the biological question I was looking for up front! I think it is worth repeating - keeping this here but also introducing the Q. in the intro.
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Oh also - BedTools is camel case here but not elsewhere.
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OK this is up to date with development as of now. Reviews very welcome! |
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link should be bedtools-example.git
And fork button link is broken as well
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Good point This seems really important. Maybe worth reversing the procedure to show that results are not the same in both directions?
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Maybe add in a quick definition of bootstrapping? It can be kind of a buzzword, so it is fun for folks to know they are doing it!
e.g. "We are able to bootstrap our results by randomizing our actual data to generate a null distribution of CpG islands across chromosomal locations. We can use this distribution to estimate how likely we would be to get these this extent of overlap by chance"
This kind of shuffle your data and see what happens approach comes up often, and I think it would be good to do some generalizing here, before the specifics of doing it for this data.
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Just to clarify for anyone coming back to this PR, it's not ready for merging and needs some more work (which I'm planning to do after the Cambridge SWC bootcamp at the end of August). In the mean time, any more comments or contributions on the work so far would be very welcome. |
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No, unfortunately this is not ready for merging. It needs maybe another half day of work and I've been struggling to find the time recently. Is there anything I can do to help smooth over #759? Should this be in it's own repo for example? |
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I think it's self-contained enough that you'll be able to redirect it to |
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Yep, sounds good to me! |
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This lesson is intended to be a 1.5 hour demo that will sit at the end of a novice python bootcamp and show learners how to apply some of their new skills to bioinformatics. Currently work in progress, contributions/suggestions very welcome!