peco
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
Bioconductor version: Release (3.19)
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 "4.4") 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 | 1.16.0 |
In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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 |
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 | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | peco_1.16.0.tar.gz |
Windows Binary | peco_1.16.0.zip |
macOS Binary (x86_64) | peco_1.16.0.tgz |
macOS Binary (arm64) | peco_1.16.0.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 |