Michael Love

I can help with this. I would argue for practical reasons as well as semantic reasons, it may best be implemented as separate function from `test_differential_abundance`, as typically the effect...

Another good effect size ranking method that could be included is: http://bioconductor.org/packages/release/bioc/html/topconfects.html https://github.com/pfh/topconfects

Could @sa-lee or @lawremi give me some pointers on where I should start, if I were to look into this?

I took a shot at this here: https://github.com/mikelove/plyranges/commit/a0dd1aba57ade82c2624665d5f97d895605b93f4 If this looks alright, I can add an example and tests. ``` > x % as_granges() > x GRanges object with 3...

tximport doesn’t modify abundances. So when you write out those matrices (as far as tximport is concerned) they would be unchanged from Salmon TPM column.