Lambda Moses

The barcodes are supposed to be 11 bp right? Are the barcodes in the whitelist 11 bp when you inspect it? One hypothesis, and I don't know if it's right,...

There's a GitHub issue about this and it's more appropriate to discuss it there: https://github.com/velocyto-team/velocyto.R/issues/23 I have never encountered this error myself, but `debug(show.velocity.on.embedding.cor)` might help you to find what...

The error message is self-explanatory. This is an error because if you want a gene count matrix, you need to translate the transcripts in the equivalence classes into genes, which...

To be honest, I don't know since I did not build that version and usually I build the index myself with whatever Ensembl version I choose. @sbooeshaghi Can you update...

Another important thing: The Bioconductor 3.11 version of `BUSpaRse` by default removes scaffolds and haplotypes from the `tr2g` data frame. The `tr2g_*` function not only has an option to remove...

Yes, using `cc = x$cc` helps, but it still calculates knn, transition probs, arrows, and etc. every single time, which still takes a while, though not nearly computationally expensive as...

Another suggestion for `show.velocity.on.embedding.cor`: it won't take significant change and should be pretty easy to implement. Can you give us options to customize point characters and arrow colors?

If both are replaced by the current version, then there really should be one version field in the `int_metadata` in the concatenated object, not two duplicated ones.

AdditionalPackage: https://github.com/pachterlab/SpatialFeatureExperiment

AdditionalPackage: https://github.com/pachterlab/Voyager