peco
This package is for version 3.11 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: 3.11
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 gmail.com>
citation("peco")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("peco")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("peco")| An example of predicting cell cycle phase using peco | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, GeneExpression, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcriptomics, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL (>= 3) |
| Depends | R (>= 2.10) |
| Imports | assertthat, circular, conicfit, doParallel, foreach, genlasso (>= 1.4), graphics, methods, parallel, scater, SingleCellExperiment, SummarizedExperiment, stats, utils |
| System Requirements | |
| URL | https://github.com/jhsiao999/peco |
| Bug Reports | https://github.com/jhsiao999/peco/issues |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | peco_1.0.0.tar.gz |
| Windows Binary | peco_1.0.0.zip |
| macOS 10.13 (High Sierra) | peco_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/peco |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/peco |
| Bioc Package Browser | https://code.bioconductor.org/browse/peco/ |
| Package Short Url | https://bioconductor.org/packages/peco/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |