Introduction

nf-core/stableexpression is a bioinformatics pipeline aiming to aggregate multiple count datasets (public / provided by the user) for a specific species and find the most stable genes.

It takes as main inputs :

• a species name (mandatory)
• keywords for Expression Atlas / GEO search (optional)
• a CSV input file listing your own raw / normalised count datasets (optional).

Use cases:

• find the most suitable genes as RT-qPCR reference genes for a specific species (and optionally specific conditions)
• download all Expression Atlas and / or NCBI GEO datasets for a species (and optionally keywords)

Basic usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

To search the most stable genes in a species considering all public datasets, simply run:

nextflow run nf-core/stableexpression \
   -profile <PROFILE (examples: docker / apptainer / conda / micromamba)> \
   --species <SPECIES (examples: arabidopsis_thaliana / "drosophila melanogaster")> \
   --outdir <OUTDIR (example: ./results)>

More advanced usage

For more specific scenarios, like:

• fetching only specific conditions
• using your own expression dataset(s)

please refer to the usage documentation.

Profiles

See here for more information about profiles.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Support us

If you like nf-core/stableexpression, please make sure you give it a star on GitHub.

Credits

nf-core/stableexpression was originally written by Olivier Coen.

Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #stableexpression channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.