The pipelines were tested with Python3.6.5, Nextflow v20.10.0 and
numpy==1.16.1
pandas==1.1.5
- Clone repo
- Add path to
go.obo
file ingo_config.sh
- Run
bash go_config.sh
The folders input
and nextflow_config
currently contain example data. Refer to this to check data formats.
- Replace the example data
./input/
with your own. - Run
bash preprocess_go_data.sh
(replacego_gene.tsv
with the filename of your input GO annotation file). - Replace the input files in
nextflow_config/vHRR_single.config
ornextflow_config/vHRR_multiple.config
with your filenames and adapt the nextflow parameters to fit your needs and system. - For a single atlas: run
bash vHRR_single.sh
. For multiple atlases: runbash vHRR_multiple.sh
.
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