[Bioc-devel] New ExperimentHub resource and some related questions

Aaron Lun infinite@monkey@@with@keybo@rd@ @ending from gm@il@com
Thu Dec 20 13:00:20 CET 2018

I presume your package is not actually called “SingleCell” (in point 1). This would be pretty confusing wjem compared to the simpleSingleCell package, the SingleCellExperiment package, and the SingleCell biocViews term itself. It would probably make more sense to call it BUStoolsR or some other appropriate pun (e.g., RBUS, which is funniest when it gets to version 3.8.0.).

Also, at first glance, the BUS format seems pretty similar to 10X’s molecule information file, for which the DropletUtils package has a series of reader functions. You may find some of the code there useful for your package. I might also add a readBUS() function to DropletUtils if this turns out to be a popular format for droplet data, though TBH the sparse matrix is a much more common starting point.


> On 20 Dec 2018, at 01:42, Lu, Dongyi (Lambda) <dlu2 using caltech.edu> wrote:
> Hi everyone,
> I’m writing a package (biocViews SinigleCell) that converts files of the BUS format (standing for Barcode, UMI, Set, see https://www.biorxiv.org/content/early/2018/11/21/472571) into a sparse matrix in R that can be used in Seurat and SingleCellExperiment. In order to write the examples and the vignette, I’m also putting the data itself into a package for ExperimentHub. The data used here are some mixed human and mouse cells from 10x. Here are my questions:
>  1.  In the documentation for `ExperimentHubData::makeExperimentHubMetadata`, the fields `RDataClass` and `DispatchClass` are required. However, this accompanying dataset package is meant to download text files (generated by command line tools outside R) to disk rather than into the R session, and it’s the job of the SingleCell package to converts the text files into a sparse matrix. There is a website documenting how the command line tools were used to generate the text files. So is this dataset still appropriate for ExperimentHub?
>  2.  If it is appropriate, then what shall I put in `RDataClass` and `DispatchClass`?
> Thanks,
> Lambda
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