Code used for the analysis of the RNA-seq, ATAC-seq and ChIP-seq datasets produced in this study. Original fastq files deposited in https://ega-archive.org/, under the accession number EGAD00001009288.
Network Analyses - SpiecEasi
The Rscripts and Snakefile herein can be used to run SpiecEasi for generating networks from taxonomic counts
snakemake >= 5.3.0
Method testing and analyses of Oxford Nanopore Technology (ONT) sequencing runs
Data obtained by sequencing "generous donor B" across several runs
Original data prepared by Rashi (post-sequencing)
Initial analyses performed by CCL