Add wrapper for scran - Githubissues

YosefLab / scone

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Add wrapper for scran #70

Closed drisso closed 7 years ago

drisso commented 8 years ago

Closed by 38c19dcd02e7307b6829d0dac165c4caaf022eba in develop

mbcole commented 7 years ago

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

ckmah commented 7 years ago

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.

mbcole commented 7 years ago

I've added a non-clustering scran scaling function in 5c41e3d8fc1b95ad245ce75efb2cd47593b79844 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