Single-cell RNA-seq (scRNA-seq) technologies are broadly applied to dissect the cellular heterogeneity and expression dynamics, providing unprecedented insights into single-cell biology. Most of the scRNA-seq studies mainly focused on the dissection of cell types/states, developmental trajectory, gene regulatory network, and alternative splicing. However, besides these routine analyses, many other valuable scRNA-seq investigations can be conducted. Here, we first review cell-to-cell communication exploration, RNA velocity inference, identification of large-scale copy number variations and single nucleotide changes, and chromatin accessibility prediction based on single-cell transcriptomics data. Next, we discuss the identification of novel genes/transcripts through transcriptome reconstruction approaches, as well as the profiling of long non-coding RNAs and circular RNAs. Additionally, we survey the integration of single-cell and bulk RNA-seq datasets for deconvoluting the cell composition of large-scale bulk samples and linking single-cell signatures to patient outcomes. These additional analyses could largely facilitate corresponding basic science and clinical applications.