These bioinformatics scripts were applied to the sequences available at https://doi.org/10.15454/3DPFNJ. They are based on several softwares, including SparCC (Friedman and Alm 2012) and DADA2 (Callahan et al. 2016). The code corresponds to R and R markdown files. These scripts were used to assess the effect of the cropping system on both community and network α- and β-properties of the foliar fungal microbiota of grapevine (Pauvert et al. Microbial networks inferred from metabarcoding data lack replicability: consequences for next-generation biomonitoring, Submitted).