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digital_sorter

An R shiny application to identify cell surface markers by mimicking the FACS sorting process.

image image

Developer guide

  1. The datasets.rds put in folder data/ should be a SplitObject of seurat.

    • Could use a separated R script merge_seuratobject_addsplits_inspect.R to create the split object (split by datasets) and add "split1", "split2", "split3", "split4" based on the expression of master markers.
    • In the metadata, the annotation of cohort origins should be "dataset_origin", sample types should be "disease".
    • Metadata should contain "annotation.l1" and "annotation.l2" from reference-based annotation (Azimuth)

  2. The markerlist.rds in folder data/ should be a list including master markers of interested cancer types.

  3. The cell.surface.marker.rds in folder data/ should be a vector of cell surface markers.

    • Could be renew by function get_cell_markers() in util.R