What tool was used to generate the UMAP by the Seeker Primary Analysis Pipeline, and how many principal components were used?

We used the RunUMAP() function in the Seurat R package on the top 30 principal components (PC). If there were fewer than 30 PCs identified, we used all identified PCs. [...]

What tool and algorithm were used for clustering by the Seeker Primary Analysis Pipeline?

We used the FindClusters() function in the Seurat R package and the Louvain algorithm for clustering.  [...]

What are the default parameters (e.g., the number of principal components used and the resolution for finding clusters) to reproduce the plots in the HTML report from the Seeker Primary Analysis Pipeline?

You can find the exact parameters used in the Seeker pipeline script seeker*/bin/analysis.R line 54-85. [...]

How do I remove the background from my Seeker data?

Please see our official documentation here: https://knowledgebase.curiobioscience.com/bioinformatics/background-removal-2/ https://knowledgebase.curiobioscience.com/bioinformatics/background-removal-2/ Note : Y ou do not have to rerun the Seeker Primary Analysis P ipeline after background removal. [...]

Once I generate my Seeker pipeline output, what can I do next to analyze my data?

We have summarized https://knowledgebase.curiobioscience.com/bioinformatics/data-analysis-workflow-latest/" target="_blank an example Spatial Secondary Analysis Workflow to help get you started analyzing your Seeker data. [...]