Data

Input Data

The CSV rumen data was extracted from the paper published by Galai at al at 2024 (DOI: [10.1111/ecog.07430] (http://dx.doi.org/10.1111/ecog.07430))

The raw data of the predicted co occurrence weight Raw_data_table_all_farms is located at the hpc in - /gpfs0/shai/users/shirneho

At the start of the pipeline, two key files are required:

• data/input/rumen_mln.csv : A CSV table of ASV pairs and their co-occurrence weights; each row specifies two microbial ASVs and the strength of their association.

• data/input/fitted_asvs_phylo_tree.rds : An RDS object containing the phylogenetic tree used for imputation.

Once these inputs are in place, the pipeline will generate intermediate network outputs via HPC jobs.