biocHCA -- Notes on Bioconductor tasks for HCA 2018 meeting

Bioconductor approach to Benchmark Data Repository management and contribution

• current examples
• are any innovations needed?

SingleCellExperiment extensions

• Seurat compatibility
• Internal interoperability assurances
• Concept of separability of data object and analysis object

Parallelization of 10x workflow

• rhdf5 can be used with socket-level parallelism, how about forking?

Back-ends for large volume assay quantifications

• HDF5 local and remote
• Spark and other distributed data architectures
• Parquet, Arrow

Metadata considerations

• accommodating the HCA schema/terminology beyond files to features, cells, donors
• Does SingleCellExperiment need additional infrastructure to increase precision of provenance
• Integrating elasticsearch functionality for R users

Workflow language and cloud deployment of 10x and allied workflows

• CWL/WDL