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: 1.4.0
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
git_url: https://git.bioconductor.org/packages/geva
git_branch: RELEASE_3_15
git_last_commit: 15633b9
git_last_commit_date: 2022-04-26
Date/Publication: 2022-04-26
NeedsCompilation: no
Packaged: 2022-04-26 23:03:06 UTC; biocbuild
Author: Itamar José Guimarães Nunes [aut, cre]
    (<https://orcid.org/0000-0002-6246-4658>),
  Murilo Zanini David [ctb],
  Bruno César Feltes [ctb] (<https://orcid.org/0000-0002-2825-8295>),
  Marcio Dorn [ctb] (<https://orcid.org/0000-0001-8534-3480>)
Maintainer: Itamar José Guimarães Nunes <nunesijg@gmail.com>
Built: R 4.2.0; ; 2022-04-27 09:33:22 UTC; windows
