Package: maEndToEnd
Title: An end to end workflow for differential gene expression using
        Affymetrix microarrays
Version: 2.29.0
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
git_url: https://git.bioconductor.org/packages/maEndToEnd
git_branch: devel
git_last_commit: 31e8b13
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-27
Packaged: 2025-06-27 17:18:12 UTC; biocbuild
Author: Bernd Klaus [aut],
  Stefanie Reisenauer [aut, cre]
Maintainer: Stefanie Reisenauer <steffi.reisenauer@tum.de>
