Michael Love

Oh, if you just want to combine transcripts to gene, I believe you can do: ``` se

This means that you need to have run Salmon with Gibbs samples or bootstraps (a requirement for Swish). For future questions feel free to post to Bioc support site and...

We do have at the beginning, “Importantly, --numGibbsSamples 20 was used to generate 20 inferential replicates with Salmon’s Gibbs sampling procedure. Inferential replicates, either from Gibbs sampling or bootstrapping of...

Thanks for the feedback @pkerrwall I've updated both vignettes to provide more information as discussed above.

Tximeta will "work" for your case that it will generate an un-ranged *SummarizedExperiment*. As you are not using GENCODE, Ensembl or RefSeq, it won't automatically download the matching transcriptome metadata....

These are better for single cell datasets. Maybe read the references associated with the sum factors function, as I think they show how its better in that paper / those...

This is a good question but I think you’d get the best advice by posting to support site, as Koen and Davide would know better than I.

Sure, so I was thinking of this because of some discussion from the CWL folks about generating Methods section text with versions. Given that tximeta knows the Salmon / alevin...

Ah cool! Yeah, I guess the title of this feature request is overly ambitious. I just mean Methods section boilerplate text. I should clarify.

Thanks @ttriche and we’ll make sure to check out Arkas