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

Lu, Dongyi (Lambda) dlu2 @ending from c@ltech@edu
Thu Dec 20 02:42:39 CET 2018

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`?


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