peco
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
Bioconductor version: 3.24 · Package version: 1.25.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("peco")Details
| Maintainer | Chiaowen Joyce Hsiao <joyce.hsiao1@gmail.com> |
| Author | Chiaowen Joyce Hsiao [aut, cre], Matthew Stephens [aut], John Blischak [ctb], Peter Carbonetto [ctb] |
| License | GPL (>= 3) |
| URL | https://github.com/jhsiao999/peco |
| Bug Reports | https://github.com/jhsiao999/peco/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/peco/ |
Citation
From within R, enter citation("peco"):
Chiaowen Joyce Hsiao, Matthew Stephens. peco: A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data. doi:10.18129/B9.bioc.peco, R package version 1.25.0, https://bioconductor.org/packages/peco.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | peco_1.25.0.tar.gz |
| Windows binary (x86_64) | peco_1.25.0.zip |
| macOS binary (arm64) | peco_1.25.0.tgz |
| macOS binary (x86_64) | peco_1.25.0.tgz |
Dependencies
Depends: R (>= 3.5.0)
Imports: assertthat, circular, conicfit, doParallel, foreach, genlasso (>= 1.4), graphics, methods, parallel, scater, SingleCellExperiment, SummarizedExperiment, stats, utils