maEndToEnd
This is the development version of maEndToEnd; to use it, please install the devel version of Bioconductor.
An end to end workflow for differential gene expression using Affymetrix microarrays
Bioconductor version: Development (3.24)
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.
Author: Bernd Klaus [aut], Stefanie Reisenauer [aut, cre]
Maintainer: Stefanie Reisenauer <steffi.reisenauer at tum.de>
citation("maEndToEnd")):Bernd Klaus, Stefanie Reisenauer. maEndToEnd: An end to end workflow for differential gene expression using Affymetrix microarrays. doi:10.18129/B9.bioc.maEndToEnd, R package version 2.33.0, https://bioconductor.org/packages/maEndToEnd.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("maEndToEnd")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("maEndToEnd")| An end to end workflow for differential gene expression using Affymetrix microarrays | HTML | R Script |
| NEWS | Text |
Details
| biocViews | GeneExpressionWorkflow, Workflow |
| Version | 2.33.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | MIT + file LICENSE |
| 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 |
| Imports | |
| System Requirements | |
| URL | https://www.bioconductor.org/help/workflows/ |
See More
| Suggests | BiocStyle, knitr, devtools, rmarkdown |
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| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | maEndToEnd_2.33.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/maEndToEnd |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/maEndToEnd |
| Package Short Url | https://bioconductor.org/packages/maEndToEnd/ |
| Package Downloads Report | Download Stats |