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array

https://github.com/aravind-1512/array

Science Score: 57.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: aravind-1512
  • Language: R
  • Default Branch: main
  • Size: 14.7 MB
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Created over 4 years ago · Last pushed over 4 years ago
Metadata Files
Readme Contributing Code of conduct Citation

README.md

Arrays

A Snakemake workflow to analyse Affymetrix expression arrays

Snakemake Snakemake-Report GitHub-Actions MIT License

Contents

Overview

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.

Installation

Install Snakemake using the conda package manager:

console $ conda create -c bioconda -c conda-forge --name snakemake snakemake

Deploy the workflow to your project directory:

console $ git pull https://github.com/zifornd/arrays projects/arrays

Usage

Configure the workflow by editing the config.yaml file:

console $ nano config/config.yaml

Define the samples by editing the samples.tsv file:

console $ nano config/samples.tsv

Execute the workflow and install dependencies:

console $ snakemake --cores all --use-conda

Documentation

See the Documentation file for all configuration, execution, and output information.

Contributing

See the Contributing file for ways to get started.

Please adhere to this project's Code of Conduct.

Authors

This workflow was developed by:

Citation

See the Citation file for ways to cite this workflow.

Acknowledgements

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)

License

This workflow is licensed under the MIT license.
Copyright © 2021, Zifo RnD Solutions

Owner

  • Name: Aravindkumar Harikrishnan
  • Login: aravind-1512
  • Kind: user
  • Location: Frankfurt, Germany

Sharpening my brains through learning in every piece of activity.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Ashmore"
  given-names: "James"
title: "My Research Software"
version: 2.0.4
doi: 10.5281/zenodo.1234
date-released: 2017-12-18
url: "https://github.com/zifornd/array"

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Dependencies

.github/workflows/main.yml actions
  • actions/checkout v1 composite
  • github/super-linter v4 composite
  • snakemake/snakemake-github-action v1.22.0 composite
  • textbook/git-checkout-submodule-action 2.0.0 composite
workflow/envs/environment.yaml conda
  • bioconductor-annotationdbi
  • bioconductor-go.db
  • bioconductor-limma
  • bioconductor-oligo
  • r-ggforce
  • r-ggplot2
  • r-ggrepel
  • r-hexbin
  • r-matrixstats
  • r-pheatmap
  • r-rcolorbrewer
  • r-reshape2