scWizard: A web-based automated tool for classifying and annotating single cells and downstream analysis of single-cell RNA-seq data in cancers

The emerging number of single-cell RNA-seq (scRNA-Seq) datasets allows the characterization of cell types across various cancer types. However, there is still lack of effective tools to integrate the various analysis of single-cells, especially for making fine annotation on subtype cells within the tumor microenvironment (TME). We developed scWizard, a point-and-click tool packaging automated process including our developed cell annotation method based on deep neural network learning and 11 downstream analyses methods. scWizard used 113,976 cells across 13 cancer types as a built-in reference dataset for training the hierarchical model enabling to automatedly classify and annotate 7 major cell types and 47 cell subtypes in the TME. scWizard provides a built-in pre-training set for user’s flexible choice, and gives a higher accuracy for annotation subtypes of tumor-derived T-lymphocytes/natural killer cells (T/NK) and myeloid cells from different cancer types compared with the existing five methods. scWizard has good robustness in three independent cancer datasets, with an accuracy of 0.98 in annotating major cell types, 0.85 in annotating myeloid cell subtypes and 0.79 in annotating T/NK cell subtypes, indicting the wide applicability of scWizard in different cell types of cancers. Finally, the automatic analysis and visualization function of scWizard are presented by using the intrahepatic cholangiocarcinoma (ICC) scRNA-Seq dataset as a case. scWizard focuses on decoding TME and covers various analysis flows for cancer scRNA-Seq study, and provides an easy-to-use tool and a user-friendly interface for researchers widely, to further accelerate the biological discovery of cancer research.