jhsiao999/peco: A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data

Our methods provide a way to assign continuous cell cycle phase using single-cell RNA-seq data, and consequently, allow for identication cyclic trend of gene expression levels along the cell cycle. This package provides method and training data, including single-cell RNA-seq data collected from 6 individual cell lines of induced pluripotent stem cells (iPSCs), and also continuous cell cycle phase derived from FUCCI fluorescence imaging data. cycle_npreg_insample and cycle_npreg_outsample are the two main functions in peco. cycle_npreg_insample generates cyclic trend estimates of gene expression levels using training data, and cycle_npreg_outsample applies the estimates of cycle_npreg_insample to another gene expression dataset to infer an angle or cell cycle phase for each cell.

install.packages("remotes")
remotes::install_github("jhsiao999/peco")