
Biomedical Data Science - dluan
http://genomicsclass.github.io/book/
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randcraw
BTW, this is the resource page from Harvard's edX course, "PH525: Statistics
and R".

"An introduction to basic statistical concepts and R programming skills
necessary for analyzing data in the life sciences."

[https://www.edx.org/course/statistics-r-harvardx-
ph525-1x](https://www.edx.org/course/statistics-r-harvardx-ph525-1x)

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et2o
This looks awesome. The second half of the class is not something that I'd
expect to see done in R, so it's nice to have all of this code.

~~~
apathy
Seriously? The topics in the second half of the class are what turned R into
something notable. People would still be jerking around with Matlab or SAS
(and getting poorer results in many cases) if Gentleman hadn't decided that
microarrays were kinda interesting.

(Kids today! Get off my lawn! Rabble rabble)

~~~
et2o
But mapping and alignment in R? Genome annotation in R? I've worked in 3
institutions with a variety of bioinformaticians and that is something I've
never seen. I'd argue that R is an unusual choice for that.

Microarrays yes, but no one (should) really uses those anymore.

Don't get me wrong, I do 50-75% of what I do in R.

~~~
apathy
Mapping an alignment gets farmed out to C via rsubread, samtools, etc. as far
as annotation, anyone who doesn't use GRanges (or vcfanno, bed tools, etc) is
insane. (You shouldn't be aligning locally anyways, it's a waste of resources
in most cases. The broad migrated their workflow to Google last I heard; we do
a lot in BaseSpace.). I actually don't see the point of alignment at all for
RNA.

Your data almost certainly has batch effects, you know. At least with arrays
the prep was fully standardized. Outside of a few big shops (UBC, the Broad,
etc) it's the goddamned Wild West in terms of prep for lots of what we used to
do with microarrays, especially RNAseq.

And of course since single cell techniques are newish, nutty ideas like
designed experiments are only just beginning to dawn on people. Fisher would
be apoplectic.

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shanacarp
Kinda wierd you posted this. I've been actually looking for something similar
to this recently. Thanks!

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dajohnson89
Looks like quality material, thank you so much!

