DESCRIPTION

Encoding: UTF-8
Type: Package
Package: peco
Version: 1.1.21
Date: 2020-11-13
Title: A Supervised Approach for Predicting Cell Cycle Progression Using
    Single-Cell RNA-seq Data
Authors@R: c(person("Chiaowen Joyce","Hsiao",email="joyce.hsiao1@gmail.com", 
                    role=c("aut","cre")),
             person("Matthew","Stephens",email="stephens999@gmail.com",
	            role="aut"),
             person("John","Blischak",email="jdblischak@gmail.com",role="ctb"),
             person("Peter","Carbonetto",email="peter.carbonetto@gmail.com",
                    role="ctb"))
Description: Our methods provide a way to assign continuous cell cycle
    phase using single-cell RNA-seq data, and consequently, allow for
    identication cyclic trend of gene expression levels along the cell
    cycle. This package provides method and training data, including
    single-cell RNA-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. cycle_npreg_insample and cycle_npreg_outsample are the two
    main functions in peco. cycle_npreg_insample generates cyclic
    trend estimates of gene expression levels using training data, and
    cycle_npreg_outsample applies the estimates of
    cycle_npreg_insample to another gene expression dataset to infer
    an angle or cell cycle phase for each cell.
URL: https://github.com/jhsiao999/peco
BugReports: https://github.com/jhsiao999/peco/issues
License: GPL (>= 3)
Depends: R (>= 2.10)
Imports:
    assertthat,
    circular,
    conicfit,
    doParallel,
    foreach,
    genlasso (>= 1.4),
    graphics,
    parallel,
    scater,
    SingleCellExperiment,
    SummarizedExperiment,
    stats,
    utils
Suggests: 
    knitr,
    rmarkdown
biocViews:
    Sequencing,
    RNASeq,
    GeneExpression,
    Transcriptomics,
    SingleCell,
    Software,
    StatisticalMethod,
    Classification,
    Visualization
LazyData: true
NeedsCompilation: no
VignetteBuilder: knitr
RoxygenNote: 7.1.1