ribiosExpression/DESCRIPTION at master · bedapub/ribiosExpression · GitHub

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Package: ribiosExpression
Type: Package
Title: Data Structures and Utilities for Gene Expression Analysis
Version: 1.3.5
Authors@R:
  person(given = "Jitao David",
         family = "Zhang",
         role = c("aut", "cre"),
         email = "jitao_david.zhang@roche.com",
         comment = c(ORCID="0000-0002-3085-0909"))
Description: Provides data structures and utility functions for gene expression
    analysis. It includes the DesignContrast class for representing study
    designs and contrasts used in differential expression analysis, functions
    for importing and exporting expression data in GCT/CLS formats, tools for
    probeset summarization and filtering, and interfaces to limma-based
    differential gene expression workflows. The package works with Biobase
    ExpressionSet objects and integrates with the limma framework.
Depends: R (>= 4.1.2)
Imports:
    methods,
    stats,
    utils,
    Biobase,
    ribiosIO (>= 1.0-18),
    ribiosUtils (>= 1.0-5),
    ribiosPlot,
    limma,
    ribiosArg,
    Matrix,
    ribiosAnnotation (>= 1.0-8),
    ComplexHeatmap,
    circlize,
    openxlsx
Suggests:
    testthat,
    grid,
    BiocStyle,
    knitr,
    rmarkdown
License: GPL-3
Encoding: UTF-8
Additional_repositories: https://bedapub.r-universe.dev
URL: https://github.com/bedapub/ribiosExpression
BugReports: https://github.com/bedapub/ribiosExpression/issues
biocViews: GeneExpression, DifferentialExpression, Microarray,
    DataImport, Visualization
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Collate:
    'AllClasses.R'
    'AllGenerics.R'
    'AllMethods.R'
    'DesignContrast.R'
    'annotate.R'
    'assertFullRank.R'
    'filter.R'
    'fixDesignMatrixColnames.R'
    'import.R'
    'io_gct_cls.R'
    'io_gmt.R'
    'io_tab.R'
    'limmaDgeTable.R'
    'mergeEset.R'
    'obsolete.R'
    'readAnnotationFile.R'
    'readFKtable.R'
    'removeAllZeroVar.R'
    'ribiosExpression-package.R'
    'ribiosExpressionSet.R'
    'sniffFeatureType.R'
    'splitPCA.R'
    'summarizeProbesets.R'
    'summarizeSamples.R'
    'transformations.R'
    'truncateDgeTable.R'
    'writeVarMetadata.R'
Remotes:
    github::bedapub/ribiosIO,
    github::bedapub/ribiosPlot,
    github::bedapub/ribiosArg,
    github::bedapub/ribiosAnnotation