Dear developers, Both scater and scran will be migrating to the SingleCellExperiment class (https://bioconductor.org/packages/SingleCellExperiment) in the next BioC release. This is based on a SummarizedExperiment and provides a more modern user interface, as well as supporting different matrix representations (e.g., dgCMatrix, HDF5Matrix).
We note that there are a number of Bioconductor packages that depend on/import/suggest scater or scran, which we have listed below: scDD scone SIMLR splatter Glimma SC3 phenopath switchde To the maintainers of these packages, we advise switching from SCESet to SingleCellExperiment as soon as possible; the former will be deprecated in the next release cycle. There are several things to note here: - The SCESet previously contained a number of slots relating to distances and clustering results. These are no longer present in the SingleCellExperiment, in line with the minimalist design philosophy of that package. If these are necessary, we suggest extending the SingleCellExperiment class in your own packages(*). - For packages that depend directly on methods in scater or scran, a number of methods have been removed. This aims to simplify the analysis workflow and code maintenance by reducing redundancy. Please ensure that your package does not need those missing methods by CHECKing it against the experimental versions(**) of these two packages: https://github.com/LTLA/scran https://github.com/davismcc/scater/tree/future If there are any issues with the switch, please let us know and we will do our best to figure out the most appropriate fix. Regards, Aaron, Davis and Davide (*): If there is popular demand for some slots, we may consider including it in the base SingleCellExperiment object. (**): These versions are highly experimental and fluid, and results are likely to be unstable over the coming month. Nonetheless, if something is breaking, it is best that we know sooner rather than later. Or in other words, don't start complaining when it's close to release time. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
