A Snakemake workflow to analyse Affymetrix expression arrays
This workflow is used to analyse Affymetrix expression arrays at the probe level. It performs quality control, differential expression analysis, and gene set testing. Batch correction and blocking are also implemented. Any expression array which has a Bioconductor annotation package is supported.
Install Snakemake using the conda package manager:
$ conda create -c bioconda -c conda-forge --name snakemake snakemakeDeploy the workflow to your project directory:
$ git pull https://github.com/zifornd/arrays projects/arraysConfigure the workflow by editing the config.yaml file:
$ nano config/config.yamlDefine the samples by editing the samples.tsv file:
$ nano config/samples.tsvExecute the workflow and install dependencies:
$ snakemake --cores all --use-conda See the Documentation file for all configuration, execution, and output information.
See the Contributing file for ways to get started.
Please adhere to this project's Code of Conduct.
This workflow was developed by:
See the Citation file for ways to cite this workflow.
This workflow is based on the following research article:
Klaus B and Reisenauer S. An end to end workflow for differential gene expression using Affymetrix microarrays [version 2; peer review: 2 approved]. F1000Research 2018, 5:1384 (https://doi.org/10.12688/f1000research.8967.2)
The sticker artwork was adapted from BiocStickers and Bioicons by Guillaume Paumier.
This workflow is licensed under the MIT license.
Copyright © 2021, Zifo RnD Solutions