Kent Riemondy

I wasn't able to set up ubsan/asan testing due to challenges getting dependencies installed. valgrind however reported no issues so I believe this should be ready to go. Performance is...

Thanks for your interest in clustifyr. There is no direct support for scanpy, however the AnnData objects can be converted to a SingleCellExperiment object using [zellkonverter](https://bioconductor.org/packages/release/bioc/html/zellkonverter.html). Alternatively, clustifyr supports sparseMatrices...

There is no built in support for comparing across species. One approach that you could try is to map the genes in the query and reference to a shared set...

Hi @matthewspeir , Thanks for the response. Very timely as another collaborator just requested the same feature. Here's a sketch of the idea:  A `split-view` feature is available in...

I think that would work. Would it be possible to "only show these cells" independently for each split screen?

Implementing these readers would duplicate much of the work already in bioconductor. It's not much effort to simply coerce the outputs from GenomicAlignments or rtracklayer into a tibble to use...

Many thanks for getting back to this request and for your continued work on this project. The split view that I had in mind is different than highlighting cells based...

It's not a single function yet, but it wouldn't be hard to port the code from some of my projects. I have code that generates another assay in the seurat...

Not sure if we need to implement new methods ourselves, instead we include a wrapper to call existing methods. I can work on a wrapper to cluster b-cells with `enclone`...

Thanks for your interest in the package: 1) In general we recommend using similar normalization approaches between the reference data the scRNA-seq dataset. So I would recommend just using log-transformed...