Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. The utility and summary file offered by this tool is directly comparable to CellRanger, the tool developed by 10X Genomics. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline (https://github.com/Hsu-Che-Wei/scKB) as the input of COPILOT.
Arabidopsis Root Virtual Expression eXplorer
Oryza Root Virtual Expression eXplorer
GeneSys: a deep generative model that simulates single-cell transcriptional dynamics over developmental and stress time courses, denoises and fuses heterogeneous data, and encodes biological knowledge so that users can test hypotheses in silico and prioritize the regulators that drive defined outcomes (Hsu et al., 2025, bioRxiv). Code: https://github.com/Hsu-Che-Wei/GeneSys
