maEndToEnd
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see maEndToEnd.
An end to end workflow for differential gene expression using Affymetrix microarrays
Bioconductor version: 3.8
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, cre], Stefanie Reisenauer [aut]
Maintainer: Bernd Klaus <bernd.klaus at embl.de>
citation("maEndToEnd")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 2.0.0 |
| License | MIT |
| 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 |
| Imports | |
| System Requirements | |
| URL | https://www.bioconductor.org/help/workflows/ |
See More
| Suggests | BiocStyle, knitr, devtools, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | maEndToEnd_2.0.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| 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 |