Workflows

This part contains several longer chapters describing complete workflows or comparisons of methods for individual analysis steps.

The workflow chapters each describe a complete analysis workflow for a single dataset, illustrating how the individual analysis steps fit together. For example, workflows may demonstrate an analysis for a dataset from a specific technological platform or tissue type. The workflows reuse code from the individual analysis chapters in a condensed format for consistency. For more details on individual analysis steps, see the chapters in the previous part.

The comparison chapters compare alternative methods for a specific analysis step, such as spatially-aware clustering. Methods are compared in terms of performance using a given dataset and evaluation metrics. This provides a way to showcase new methods as these are developed and implemented in the Bioconductor framework, and provides readers with information on which methods may be appropriate for their analyses.