DESCRIPTION

Package: cicero
Type: Package
Title: Predict cis-co-accessibility from single-cell chromatin accessibility data
Version: 1.17.2
Authors@R: c(
    person("Hannah", "Pliner", email = "hpliner@uw.edu", role = c("aut", "cre")), 
    person("Cole", "Trapnell", email = "coletrap@uw.edu", role = c("aut")))
Description: Cicero computes putative cis-regulatory maps from single-cell chromatin 
    accessibility data. It also extends monocle 2 for use in chromatin accessibility
    data.
Depends:
    R (>= 3.5.0),
    monocle,
    Gviz (>= 1.22.3)
License: MIT + file LICENSE
Encoding: UTF-8
Imports:
    assertthat (>= 0.2.0),
    Biobase (>= 2.37.2),
    BiocGenerics (>= 0.23.0),
    data.table (>= 1.10.4),
    dplyr (>= 0.7.4),
    FNN (>= 1.1),
    GenomicRanges (>= 1.30.3),
    ggplot2 (>= 2.2.1),
    glasso (>= 1.8),
    grDevices,
    igraph (>= 1.1.0),
    IRanges (>= 2.10.5),
    Matrix (>= 1.2-12),
    methods,
    parallel,
    plyr (>= 1.8.4),
    reshape2 (>= 1.4.3),
    S4Vectors (>= 0.14.7),
    stats,
    stringi,
    stringr (>= 1.2.0),    
    tibble (>= 1.4.2),
    tidyr,
    VGAM (>= 1.0-5),
    utils
RoxygenNote: 7.2.3
Suggests:
    AnnotationDbi (>= 1.38.2),
    knitr,
    markdown,
    rmarkdown,
    rtracklayer (>= 1.36.6),
    testthat,
    vdiffr (>= 0.2.3),
    covr
VignetteBuilder: knitr
biocViews: Sequencing, Clustering, CellBasedAssays, ImmunoOncology, 
    GeneRegulation, GeneTarget, Epigenetics, ATACSeq, SingleCell
LazyData: true