Data and code for "Bacterial interactions underpin worsening lung function in cystic fibrosis-associated infections".

The raw data generated in this study have been previously deposited in the European Nucleotide Archive under the accession numbers PRJEB52183 and PRJEB62148, and in the Sequence Read Archive under BioProject numbers PRJNA1113124 and PRJNA1113142, with extra samples used in this study in PRJNA1112360. For ease, however, they are all available in this Dropbox link with all the control wells.Files included here are:merged_data_44_blast_ordered - the dataset used in this analysisCF_interaction_code_shared - R code to recreate the analysis and figures presented in the manuscriptCF_interaction_code_initial_clean_shared - R code for the initial clean-up and merging of the ASV, metadata, and taxa data sets. Culminates in the creation of "merged_data_44_blast_ordered.csv".CF_interaction_code_shared_PR - R code to recreate the analysis and figures presented in the manuscript edited to include reviewer's requested amendments.DATASET_unclean - contains all of the metadata for the samples used.taxa_44_blast - contains all of the ASV sequences and taxa alignments, after manually blasting the unassigned sequences.ASV_table_44 - contains all the read data for the samples and sequence.