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
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev perl libsasl2-dev
Repository: https://bedapub.r-universe.dev
Date/Publication: 2026-06-15 13:54:40 UTC
RemoteUrl: https://github.com/bedapub/ribiosExpression
RemoteRef: HEAD
RemoteSha: 51b5fd3271db0eaf37a3cc204d070a990e6fc623
NeedsCompilation: no
Packaged: 2026-06-15 16:03:46 UTC; root
Author: Jitao David Zhang [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3085-0909>)
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>