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.

Getting started

Package details

Bioconductor views Classification GeneExpression RNASeq Sequencing SingleCell Software StatisticalMethod Transcriptomics Visualization
LicenseGPL (>= 3)
URL https://github.com/jhsiao999/peco
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
jhsiao999/peco documentation built on Nov. 21, 2020, 5:34 p.m.