Skip to content

Differential gene expression analysis and pathway analysis of RNAseq data

License

Notifications You must be signed in to change notification settings

WackerO/rnadeseq

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

qbic-pipelines/rnadeseq

Downstream differential gene expression analysis with DESeq2 package.

Nextflow install with bioconda Docker DOI

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Documentation

The qbic-pipelines/rnadeseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Credits

qbic-pipelines/rnadeseq was written by Gisela Gabernet (@ggabernet), Silvia Morini (@silviamorins) and Oskar Wacker (@WackerO), at QBiC. The DESeq2 scripts were originally written by @qbicStefanC.

The pipeline structure is based on the template by the nf-core project. For more information, please check out the nf-core website.

If you would like to contribute to this pipeline, please see the contributing guidelines.

About

Differential gene expression analysis and pathway analysis of RNAseq data

Resources

License

Code of conduct

Stars

Watchers

Forks

Packages

No packages published

Languages

  • Nextflow 72.3%
  • Python 9.5%
  • TeX 8.3%
  • R 6.4%
  • HTML 2.2%
  • Dockerfile 0.9%
  • CSS 0.4%