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.

We have some stuff in `fishpond` for import and processing, and welcome to consider other things to go in there. Just need docs and tests really. There’s even some new...

Great!

I would say that having a data.frame instead of matrix in the SummarizedExperiment is not typical.

Yup. I see correlations around .8 which seems reasonable. Imagine: gene X has count 100 and transcript length 1,000 gene Y has count 100 and transcript length 10,000 these have...

There is a long literature about why we use counts or CPM (in either case, optionally with an effective transcript length offset) instead of raw TPM for statistical modeling. Using...