Dear Biostars community,
I was just wondering if there are any differential expression analysis tools which can be used downstream of
Salmon, which incorporates abundance estimate variation information when either the
--numGibbsSamples are used when running
The salmon documentation states the following:
Such estimates can be useful for downstream (e.g. differential expression) tools that can make use of such uncertainty estimates.
Do we know of any tools which will incorporate this transcript abundance estimate variation information when calling differential expression at the transcript-level i.e (DTE - differential transcript expression).
Sleuth does something along these lines with
kallisto output, but I was just wondering if there was any tools that processed
Salmon output in a similar manner. I have looked at the vignette, and I do not think
DeSeq2 (version 1.22.2 at the time of writing) does this, unless I am mistaken?