Package: TraRe
Title: Transcriptional Rewiring
Version: 1.6.3
URL: https://github.com/ubioinformat/TraRe/tree/master
Authors@R: 
    c(person(given = "Jesus",
           family = "de la Fuente Cedeño",
           role = c("aut", "cre","cph"),
           email = "jdelafuentec@unav.es",
           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 Goñi",
	   role = c("ctb"),
	   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
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
git_url: https://git.bioconductor.org/packages/TraRe
git_branch: RELEASE_3_16
git_last_commit: 3acb353
git_last_commit_date: 2022-12-12
Date/Publication: 2022-12-12
Packaged: 2022-12-13 02:57:23 UTC; biocbuild
Author: Jesus de la Fuente Cedeño [aut, cre, cph]
    (<https://orcid.org/0000-0003-1856-2469>),
  Mikel Hernaez [aut, cph, ths] (<https://orcid.org/0000-0003-0443-2305>),
  Charles Blatti [aut, cph] (<https://orcid.org/0000-0002-4683-6271>),
  Zikun [ctb] (<https://orcid.org/0000-0002-9933-9658>),
  Irene Marin Goñi [ctb] (<https://orcid.org/0000-0002-5060-0712>)
Maintainer: Jesus de la Fuente Cedeño <jdelafuentec@unav.es>
Built: R 4.2.2; x86_64-w64-mingw32; 2022-12-13 12:47:34 UTC; windows
ExperimentalWindowsRuntime: ucrt
Archs: x64
