Task 1: provide a unified representation of single-cell data

Challenges:

Proposed solutions:

Useful Bioconductor packages and other resources:

Task 2: scale-up of existing tools / implementation of tools to handle large-scale datasets

Challenges:

Proposed solutions:

Useful Bioconductor packages and other resources:

Interested in contributing? Join the slack channel:

https://community-bioc.slack.com

Discussion points

  1. Benchmark (canonical datasets)
  2. Splatter (simulations of scRNA-seq)
  3. What to do next?
  4. BigDataAlgorithms: define scope, what functionalities we want
  1. Prior art in astronomy, etc?
  1. Visualization?
  2. Multi assay?
  1. People are running single-cell assays that generate multiple types of data (e.g., RNA expression and methylation) from each single-cell.
  2. Can store each assay in a SingleCellExperiment and then put inside a MultiAssayExperiment to link up the row and column metadata.
  1. Multiple samples--list of SingleCellExperiments vs giant joined SingleCellExperiment.  Can we learn from flowSet?