Package: ribiosNGS
Type: Package
Title: Differential gene expression analysis for next-generation
        sequencing data in the 'ribios' suite
Version: 1.0.0
Authors@R: 
  c(person(given = "Jitao David",
         family = "Zhang",
         role = c("aut", "cre", "ctb"),
         email = "jitao_david.zhang@roche.com",
         comment = c(ORCID="0000-0002-3085-0909")),
    person(given="Ailu",
           family="Mading",
           role="ctb"))
Description: Provides a comprehensive workflow for differential gene
        expression analysis of RNA-seq data using 'edgeR' and
        'limma'-voom pipelines. The package supports count filtering,
        normalization, surrogate variable analysis, batch correction,
        and visualization including volcano plots, smear plots, and
        PCA. It integrates with the 'ribios' suite of packages and is
        designed for reproducible bioinformatics analyses.
Depends: R (>= 4.4.0),
Imports: BiocGenerics, ribiosExpression (>= 1.2.0), edgeR,
        ribiosAnnotation (>= 3.6.0), ribiosUtils, methods, Biobase,
        lattice, ribiosIO (>= 1.0-60), ribiosPlot (>= 1.2-9), graphics,
        limma, readr, readxl, magrittr, sva, dplyr, vsn, made4,
        ggplot2, rlang, gt, scales, UpSetR, ggrepel, reshape2
Suggests: testthat, ggpubr, tibble, knitr, rmarkdown, BiocStyle
biocViews: DifferentialExpression, GeneExpression, RNASeq,
        Transcriptomics
License: GPL-3
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.3.3
Collate: 'utils.R' 'ribiosNGS-package.R' 'AllClasses.R' 'AllGenerics.R'
        'AllMethods.R' '20210217-toribios.R' 'DGEListToLongTable.R'
        'EdgeObject.R' 'annotateMethods.R' 'pseudoT.R' 'appendZScore.R'
        'edgeR-funcs.R' 'dge.R' 'dgeTable.R' 'edgeR-slurm-lsf.R'
        'eset2DGEList.R' 'exportEdgeResult.R' 'filterByCPM.R'
        'knockdown.R' 'logFCmatrix.R' 'logFCpca.R' 'mergeDGEList.R'
        'minGroupCount.R' 'mps-io.R' 'normalize.R' 'pca.R'
        'plotMethods.R' 'plotTopSigGenes.R' 'readBiokitAsDGEList.R'
        'readFeatureAnnotationForEdgeR.R'
        'readSampleAnnotationForEdgeR.R' 'renameContrast.R'
        'split.DGEList.R' 'staticGeneLevelPlots.R' 'sva.R'
        'svaseqRemove.R' 'topDgeExpression.R' 'tpm.R' 'voomLimma.R'
        'writeBiokitSampleAnnotation.R' 'writeDGEList.R'
Remotes: github::bedapub/ribiosExpression,
        github::bedapub/ribiosAnnotation, github::bedapub/ribiosUtils,
        github::bedapub/ribiosIO, github::bedapub/ribiosPlot
Additional_repositories: https://bedapub.r-universe.dev
URL: https://github.com/bedapub/ribiosNGS
BugReports: https://github.com/bedapub/ribiosNGS/issues
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev perl libsasl2-dev libnode-dev libx11-dev
        zlib1g-dev
Repository: https://bedapub.r-universe.dev
Date/Publication: 2026-02-15 11:40:09 UTC
RemoteUrl: https://github.com/bedapub/ribiosNGS
RemoteRef: HEAD
RemoteSha: 90513e37c7ab00a23dff38258a29b2e7e4589443
NeedsCompilation: no
Packaged: 2026-06-15 16:05:26 UTC; root
Author: Jitao David Zhang [aut, cre, ctb] (ORCID:
    <https://orcid.org/0000-0002-3085-0909>),
  Ailu Mading [ctb]
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>