DOI: 10.18129/B9.bioc.peco  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see peco.

A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

Bioconductor version: 3.17

Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently, allows to identify cyclic trend of gene expression levels along the cell cycle. This package provides method and training data, which includes scRNA-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.

Author: Chiaowen Joyce Hsiao [aut, cre], Matthew Stephens [aut], John Blischak [ctb], Peter Carbonetto [ctb]

Maintainer: Chiaowen Joyce Hsiao <joyce.hsiao1 at>

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biocViews Classification, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcriptomics, Visualization
Version 1.12.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License GPL (>= 3)
Depends R (>= 3.5.0)
Imports assertthat, circular, conicfit, doParallel, foreach, genlasso (>= 1.4), graphics, methods, parallel, scater, SingleCellExperiment, SummarizedExperiment, stats, utils
Suggests knitr, rmarkdown
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