vHRR: co-expression based gene function prediction

Requirements

The pipelines were tested with Python3.6.5, Nextflow v20.10.0 and

numpy==1.16.1
pandas==1.1.5

Installation

1. Clone repo
2. Add path to go.obo file in go_config.sh
3. Run bash go_config.sh

Run

The folders input and nextflow_config currently contain example data. Refer to this to check data formats.

1. Replace the example data ./input/ with your own.
2. Run bash preprocess_go_data.sh (replace go_gene.tsv with the filename of your input GO annotation file).
3. Replace the input files in nextflow_config/vHRR_single.config or nextflow_config/vHRR_multiple.config with your filenames and adapt the nextflow parameters to fit your needs and system.
4. For a single atlas: run bash vHRR_single.sh. For multiple atlases: run bash vHRR_multiple.sh.

Citation

If you publish results generated using vHRR, please cite:

Depuydt, T. and Vandepoele, K. (2021), Multi-omics network-based functional annotation of unknown Arabidopsis genes. Plant J. Accepted Author Manuscript. https://doi.org/10.1111/tpj.15507