[Bioc-devel] transitioning scater/scran to SingleCellExperiment

[Aaron Lun]

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.