DESCRIPTION

Package: ribiosNGS
Type: Package
Title: Utilities for next-generation sequencing data analysis in ribios
Version: 1.4.8.9005
Date: 2023-10-03
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"),
    person("F.Hoffmann-La Roche AG", role="cph"))
Description: NGS tasks in ribios, primarily differetial gene expression
    analysis.
Depends:
    R (>= 2.1.0),
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,
    ggpubr,
    rlang,
    gt,
    scales,
    UpSetR,
    ggrepel,
    reshape2
Suggests:
    testthat,
    tibble
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.2.3
Collate: 
    '20210217-toribios.R'
    'ribiosNGS-package.R'
    'AllClasses.R'
    'AllGenerics.R'
    'utils.R'
    'AllMethods.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'
URL: https://github.com/bedapub/ribiosNGS
BugReports: https://github.com/bedapub/ribiosNGS/issues
Remotes:
    github::bedapub/ribiosExpression,
    github::bedapub/ribiosAnnotation,
    github::bedapub/ribiosUtils,
    github::bedapub/ribiosIO,
    github::bedapub/ribiosPlot