Detection of cell markers from single cell RNA-seq with sc2marker

Single cell sequencing allow the detection of rare cell types in complex tissues. The detection of markers for these cell types are useful for further biological analysis as flow cytometry and imaging for either physical isolation or spatial characterization of these cells.  Nevertheless, only few computational approaches consider the problem of selection of small marker genes from single cell sequencing so far. We propose here sc2marker, which is based on a weighted residual measure and database of proteins with antibodies, to select markers for imaging or flow cytometry. We evaluate the performance of sc2marker on single cell data of immune and stromal cells, which shows its superior performance in both time and accuracy in ranking known markers in  contrast to competing methods.