peco
This is the development version of peco; for the stable release version, see peco.
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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 | |
| 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_1.25.0.tar.gz |
| Windows Binary (x86_64) | peco_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | peco_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | peco_1.25.0.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 |