Package: geva
Type: Package
Title: Gene Expression Variation Analysis (GEVA)
Description: Statistic methods to evaluate variations of differential
        expression (DE) between multiple biological conditions. It
        takes into account the fold-changes and p-values from previous
        differential expression (DE) results that use large-scale data
        (*e.g.*, microarray and RNA-seq) and evaluates which genes
        would react in response to the distinct experiments. This
        evaluation involves an unique pipeline of statistical methods,
        including weighted summarization, quantile detection, cluster
        analysis, and ANOVA tests, in order to classify a subset of
        relevant genes whose DE is similar or dependent to certain
        biological factors.
Version: 1.18.0
Authors@R: 
    c(person(given = "Itamar José",
             family = "Guimarães Nunes",
             role = c("aut", "cre"),
             email = "nunesijg@gmail.com",
             comment = c(ORCID = "0000-0002-6246-4658")),
      person(given = "Murilo",
             family = "Zanini David",
             email = "zanini.murilo@gmail.com",
             role = "ctb"),
      person(given = "Bruno",
             family = "César Feltes",
             email = "bcfeltes@gmail.com",
             role = "ctb",
             comment = c(ORCID = "0000-0002-2825-8295")),
      person(given = "Marcio",
             family = "Dorn",
             email = "mdorn@inf.ufrgs.br",
             role = "ctb",
             comment = c(ORCID = "0000-0001-8534-3480")))
URL: https://github.com/sbcblab/geva
BiocType: Software
biocViews: Classification, DifferentialExpression, GeneExpression,
        Microarray, MultipleComparison, RNASeq, SystemsBiology,
        Transcriptomics
License: LGPL-3
Encoding: UTF-8
Depends: R (>= 4.1)
Imports: grDevices, graphics, methods, stats, utils, dbscan,
        fastcluster, matrixStats
Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat
        (>= 3.0.0)
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Collate: 'stringhelpers.R' 'callhelpers.R' 'vectorhelpers.R'
        'printhelpers.R' 'asserts.R' 'usecasechecks.R' 'plotting.R'
        'dochelpers.R' 'generics.R' 'classhelpers.R' 'c_SVTable.R'
        'c_GEVAGroupSet.R' 'c_GEVACluster.R' 'funhelpers.R' 'linq.R'
        'c_TypedList.R' 'c_SVAttribute.R' 'c_GEVAInput.R'
        'c_GEVASummary.R' 'c_GEVAGroupedSummary.R' 'c_GEVAQuantiles.R'
        'c_GEVAQuantilesAdjusted.R' 'c_GEVAResults.R' 'summarization.R'
        'clusteringbase.R' 'matrixhelpers.R' 'statmath.R'
        'dclustering.R' 'quantiles.R' 'factoring.R' 'scoremerge.R'
        'finalize.R' 'geva-package.R' 'hclustering.R' 'idealtesting.R'
        'input.R'
Config/testthat/edition: 3
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:07:07 UTC
RemoteUrl: https://github.com/bioc/geva
RemoteRef: RELEASE_3_22
RemoteSha: c291ceb59b475ac7b42bf9416771f049978e8bad
NeedsCompilation: no
Packaged: 2025-11-20 07:27:27 UTC; root
Author: Itamar José Guimarães Nunes [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6246-4658>),
  Murilo Zanini David [ctb],
  Bruno César Feltes [ctb] (ORCID:
    <https://orcid.org/0000-0002-2825-8295>),
  Marcio Dorn [ctb] (ORCID: <https://orcid.org/0000-0001-8534-3480>)
Maintainer: Itamar José Guimarães Nunes <nunesijg@gmail.com>
Built: R 4.5.2; ; 2025-11-20 07:29:10 UTC; windows
