Import spatial transcriptomics output as SpatialExperiment

[allyhawkins]

Following quantification of the Spatial transcriptomics libraries, we will need to have a second process that imports that output into R as a SpatialExperiment and then writes that outputs those objects as RDS files.

To me it only makes sense here to only have one file that includes the filtered results, rather than unfiltered and filtered results.
Following creation of the SpatialExperiment I also think we want to filter to only include spots that overlap the tissue or is there rationale to include all spots?

**If we use Alevin-fry and Spaceranger for quantification, this issue should be dependent on addition of a function to scpcaTools to merge output from both of those tools to create the SpatialExperiment.

[allyhawkins]

Since we are no longer using Alevin-fry right now and only Spaceranger, we don't need to import the ST output as a SpatialExperiment at this point. Going ahead and closing this.