Add wrapper for scran

Question

Add wrapper for scran

Closed this issue 7 years ago · 4 comments

drisso commented 8 years ago

Answer 1 · 2016-11-04T23:48:26.000Z

Closed by 38c19dc in develop

Answer 2 · 2017-01-17T00:07:45.000Z

Must re-introduce @ckmah 's wrapper with additional automation / modified argument interface

Answer 3 · 2017-01-19T00:41:13.000Z

There is a case where the internal clustering step quickCluster may break if there are too few cells (less than default minimum threshold of 200). Similarly computeSumFactors has a minimum threshold of some sort as well. @mbcole If this isn't too urgent I would be happy to investigate.

Answer 4 · 2017-04-06T06:59:41.000Z

I've added a non-clustering scran scaling function in 5c41e3d but I think we will ultimately want to pass arguments to a wrapper similar to your original. I've added a new issue for this: #84