CeleScope™ is an analysis pipeline developed at Singleron to process massively parallel single-cell RNA-seq data. With a single command, CeleScope™ automatically generates gene expression matrix and QC report for each dataset. The pipeline first extracts cell barcodes (CB), performs CB error corrections, and then removes low quality reads before aligning reads to the reference genome. UMIs per gene per cell are counted and corrected to generate the gene expression matrix. A html report is also provided to the users, containing QC metrics for each analysis step.