Package: maEndToEnd
Title: An end to end workflow for differential gene expression using
        Affymetrix microarrays
Version: 2.32.0
Date: 2024-01-12
Authors@R: c(person(role="aut", "Bernd", "Klaus", email = "bernd.klaus@embl.de"),
             person(role=c("aut", "cre"), "Stefanie", "Reisenauer", email = "steffi.reisenauer@tum.de"))
Description: In this article, we walk through an end-to-end Affymetrix
        microarray differential expression workflow using Bioconductor
        packages. This workflow is directly applicable to current
        "Gene" type arrays, e.g. the HuGene or MoGene arrays, but can
        easily be adapted to similar platforms. The data analyzed here
        is a typical clinical microarray data set that compares
        inflamed and non-inflamed colon tissue in two disease subtypes.
        For each disease, the differential gene expression between
        inflamed- and non-inflamed colon tissue was analyzed. We will
        start from the raw data CEL files, show how to import them into
        a Bioconductor ExpressionSet, perform quality control and
        normalization and finally differential gene expression (DE)
        analysis, followed by some enrichment analysis.
Depends: R (>= 3.5.0), Biobase, oligoClasses, ArrayExpress,
        pd.hugene.1.0.st.v1, hugene10sttranscriptcluster.db, oligo,
        arrayQualityMetrics, limma, topGO, ReactomePA, clusterProfiler,
        gplots, ggplot2, geneplotter, pheatmap, RColorBrewer, dplyr,
        tidyr, stringr, matrixStats, genefilter, openxlsx, Rgraphviz,
        enrichplot
Suggests: BiocStyle, knitr, devtools, rmarkdown
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: GeneExpressionWorkflow
NeedsCompilation: no
URL: https://www.bioconductor.org/help/workflows/
Workflow: True
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:43:24 UTC
RemoteUrl: https://github.com/bioc/maEndToEnd
RemoteRef: RELEASE_3_23
RemoteSha: 4b49cad5e8cf18e1af79fdc06816b87ca8c0706f
Packaged: 2026-10-07 14:48:13 UTC; root
Author: Bernd Klaus [aut],
  Stefanie Reisenauer [aut, cre]
Maintainer: Stefanie Reisenauer <steffi.reisenauer@tum.de>