Rmarkdown report for the analysis to go with the manuscript "Host-plasmid network structure in wastewater is linked to antimicrobial resistance genes " by Alice Risely, Arthur Newbury, Thibault Stalder, Benno I. Simmons, Eva M. Top, Angus Buckling, and Dirk Sanders
Data generated by: Stalder et al. "Linking the resistome and plasmidome to the microbiome." The ISME journal 13.10 (2019): 2437-2446.
CODE
Code is in html and pdf format. To view the html format, you will need to download the file to open. Code is split into two files: 1) Hi-C processing in R, and 2) Network analysis in R.
DATA
plasmid_ps_clustered_genomad_final.RDS == bacteria-plasmid association matrix and metadata stored as a phyloseq object cluster_membership_genomad.RDS == plasmid contig metadata phylophlan.tre.treefile == Phylogenetic tree of bacteria phylophlan_taxonomy_updated.csv == Taxonomy of bacteria