Project overview¶
Single-cell tertiary analyses include step such as:
- expression matrix normalisation
- cell filtering
- computation of dimension reductions
- clustering itself
These steps may be implemented in a variety of ways including stand-alone tools, scripts, or R package functions. To compare equivalent logical steps between workflows, and to ‘mix and match’ those components for optimal workflows is therefore a challenging excercise without additional infrastructure.
We aim to ‘componentise’ tools associated with these workflows and more importantly build standards and infrastructure to facilitate this process for others in future.
Objectives¶
- Write additional scripts where necessary to expose inividual worklow units as scripts with well-defined inputs and outputs.
- Build (programming) language-independent standards for input, output and intermediate data types.
- Make components avialable in as simple a manner as possible, via the Bioconda repository.
- Make containers available for these packages, suitable for cloud deployment.
- Make preliminary assessments of individual workflows, components, and ‘mixed’ workflows.