DESCRIPTION

Package: NetBID2
Type: Package
Title: Network-based Bayesian Inference of Drivers, version 2
Version: 2.2.0
Authors@R: person('Xinran', 'Dong', email = 'xinran.dong@foxmail.com', role = c('aut', 'cre'))
Maintainer@R: c(
  person('Xinran', 'Dong', email = 'xinran.dong@foxmail.com'),
  person(given = "Qingfei", family = "Pan", email = "qingfei.pan@stjude.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0243-6898")))
Description: An integrative systems biology algorithm to infer drivers of phenotype based on data-driven context-specific network and Bayesian inference.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: 
    R (>= 3.6.0),
    Matrix (>= 1.2-17),
    SummarizedExperiment (>= 1.14.0),
    lme4 (>= 1.1-21),
    Biobase (>= 2.38.0),
    GEOquery (>= 2.46.15),
    limma (>= 3.34.9),
    impute (>= 1.52.0),
    tximport (>= 1.6.0),
    DESeq2 (>= 1.20.0),
    ConsensusClusterPlus (>= 1.38.0),
    aricode (>= 0.1.1),
    igraph (>= 1.1.2),
    RColorBrewer (>= 1.1-2),
    plot3D (>= 1.1.1),
    plotrix (>= 3.7-3),
    umap (>= 0.2.0.0),
    ComplexHeatmap (>= 1.17.1),
    ordinal (>= 2019.4-25),
    MCMCglmm (>= 2.26),
    arm (>= 1.10-1),
    reshape (>= 0.8.7),
    biomaRt (>= 2.34.2),
    GSVA (>= 1.22.4),
    msigdbr (>= 6.2.1),
    openxlsx (>= 4.1.0),
    rmarkdown (>= 1.11),
    kableExtra (>= 1.1.0),
    rhdf5 (>= 2.28.0),
    plotly (>= 4.9.0)
Imports:
Suggests:
RoxygenNote: 7.1.1