TraRe/DESCRIPTION at master · ML4BM-Lab/TraRe · GitHub

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Package: TraRe
Title: Transcriptional Rewiring
Version: 0.99.0
URL: https://github.com/ubioinformat/TraRe/tree/master
Authors@R:
    c(person(given = "Jesus",
           family = "de la Fuente Cedeno",
           role = c("aut", "cre","cph"),
           email = "jdlfuentec@gmail.com",
           comment = c(ORCID = "0000-0003-1856-2469")),
    person(given = "Mikel",
           family = "Hernaez",
           role = c("aut", "cph","ths"),
           email = "mhernaez@unav.es",
           comment = c(ORCID = "0000-0003-0443-2305")),
    person(given = "Charles",
           family = "Blatti",
           role = c("aut", "cph"),
           email = "blatti@illinois.edu",
           comment = c(ORCID = "0000-0002-4683-6271")),
    person(given = "Zikun",
           family = "",
           role = c("ctb"),
           email = "",
           comment = c(ORCID = "0000-0002-9933-9658")),
    person(given="Irene",
	   family = "Marin Goni",
	   role = c("aut"),
	   email = "imarin.4@alumni.unav.es",
	   comment = c(ORCID = "0000-0002-5060-0712")))
Description: TraRe (Transcriptional Rewiring) is an R package which contains the necessary tools to carry out several functions.
             Identification of module-based gene regulatory networks (GRN); score-based classification of these modules via
             a rewiring test; visualization of rewired modules to analyze condition-based GRN deregulation and drop out genes
             recovering via cliques methodology. For each tool, an html report can be generated containing useful information about
             the generated GRN and statistical data about the performed tests. These tools have been developed considering sequenced data (RNA-seq).
Depends:
	R (>= 4.0)
Imports:
    hash,
    ggplot2,
    stats,
    methods,
    igraph,
    utils,
    glmnet,
    grDevices,
    gplots,
    gtools,
    pvclust,
    R.utils,
    dqrng,
    SummarizedExperiment,
    matrixStats,
    BiocParallel,
    scales,
    vioplot,
    viridis
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: False
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.2
biocViews: GeneRegulation, RNASeq, GraphAndNetwork, Bayesian, GeneTarget, Classification
NeedsCompilation: yes
Suggests:
    knitr,
    rmarkdown,
    BiocGenerics,
    RUnit,
    BiocStyle
VignetteBuilder: knitr
PackageStatus: Deprecated
Collate:
    'cliques_generatecliques.R'
    'compute_KL.R'
    'html_from_graph.R'
    'linker_html_summary.R'
    'linker_html_summary_functions.R'
    'linker_runlinker.R'
    'linker_runlinkernet.R'
    'linker_runphaseone.R'
    'linker_runphasetwo.R'
    'plot_functions.R'
    'preprocessing.R'
    'rewiring_create_module_summary.R'
    'rewiring_gene_level.R'
    'rewiring_html_summary.R'
    'rewiring_html_summary_functions.R'
    'rewiring_preparerewiring.R'
    'rewiring_regulon_level.R'
    'rewiring_runrewiring.R'
    'rewiring_stats_functions.R'
    'vbsr.R'
    'zzz.R'