Package: DESeqAnalysis
Title: Acid Genomics DESeq2 Analysis Utilities
Description: Toolkit for performing differential expression with DESeq2.
Version: 0.4.4
Date: 2021-08-02
Authors@R: c(
    person(
        given = "Michael",
        family = "Steinbaugh",
        email = "mike@steinbaugh.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-2403-2221")
    ),
    person(
        given = "Acid Genomics",
        role = c("cph", "fnd")
    ))
URL: https://r.acidgenomics.com/packages/deseqanalysis/,
        https://github.com/acidgenomics/r-deseqanalysis/
BugReports: https://github.com/acidgenomics/r-deseqanalysis/issues/
License: AGPL-3
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.0), basejump (>= 0.14.19), DESeq2 (>= 1.30)
Imports: AcidGenerics (>= 0.5.18), AcidPlots (>= 0.3.7), ggplot2 (>=
        3.3.5), goalie (>= 0.5.2), methods
Suggests: apeglm (>= 1.12), ashr (>= 2.2), knitr, testthat, tximport
        (>= 1.18)
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Additional_repositories: https://r.acidgenomics.com
Collate: 'AllClasses.R' 'AllGenerics.R' 'AllGenerators.R'
        'AllGlobals.R' 'alphaSummary-methods.R'
        'alphaThreshold-methods.R' 'apeglmResults-methods.R'
        'base-methods.R' 'baseMeanThreshold-methods.R'
        'coerce-methods.R' 'combine-methods.R' 'contrastName-methods.R'
        'contrastSamples-methods.R' 'correlation-methods.R' 'data.R'
        'deg-methods.R' 'degIntersection-methods.R'
        'degPerContrast-methods.R' 'deprecated.R' 'export-methods.R'
        'extract-methods.R' 'importPairwiseContrasts.R'
        'interestingGroups-methods.R' 'internal.R'
        'lfcShrink-methods.R' 'lfcShrinkType-methods.R'
        'lfcThreshold-methods.R' 'matchMetadataToFiles.R' 'package.R'
        'plotBaseMean-methods.R' 'plotCounts-methods.R'
        'plotDEGHeatmap-methods.R' 'plotDEGPCA-methods.R'
        'plotDEGStackedBar-methods.R' 'plotDEGUpset-methods.R'
        'plotHeatmap-methods.R' 'plotMA-methods.R' 'plotPCA-methods.R'
        'plotVolcano-methods.R' 'prepareTximportFiles.R'
        'results-methods.R' 'resultsDiff-methods.R'
        'resultsMatrix-methods.R' 'resultsNames-methods.R'
        'resultsTables-methods.R' 'sampleData-methods.R'
        'show-methods.R' 'topTables-methods.R'
        'transformType-methods.R' 'updateObject-methods.R'
Author: Michael Steinbaugh [aut, cre] (<https://orcid.org/0000-0002-2403-2221>),
  Acid Genomics [cph, fnd]
Maintainer: Michael Steinbaugh <mike@steinbaugh.com>
Built: R 4.1.0; ; 2021-08-02 17:36:02 UTC; unix
