Giters

qbic-pipelines / rnadeseq

Differential gene expression analysis and pathway analysis of RNAseq data

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

deseq2nextflowpathway-analysispipelinernaseq

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

deseq2nextflowpathway-analysispipelinernaseq

License:MIT License

Languages

Language:Nextflow 59.4%Language:Groovy 17.5%Language:Python 7.7%Language:TeX 6.7%Language:R 5.3%Language:HTML 2.4%Language:Dockerfile 0.7%Language:CSS 0.3%