Data Repo for Prebiotic activity of lactulose optimizes gut metabolites and prevents systemic infection in liver disease patients

Folder structure

code: contains all R scripts for generating heatmap, volcano plots and/or taxonomy barplots, etc. Scripts are organized by number. Resultant plots are labeled with same number as the script.
results: contains all unmodified graphs in PDF format. Graphs published along with the paper have been slightly rearranged and beautified in Adobe Illustrator.
data: contains raw or derived data or template files

LD847_HD22.meta.quant.metabolomics.csv: the most important file. It contains clinical variables, such as stool consistency, lactulose, Bifidobacterium group (10% is the cutoff), SBP, bacteremia status, or metagenomically derived toxin RPKM values, quant metabolomics readings from SCFA (unit: mM) and bile acid (unit: ug/ml) panels, etc.
LD847_HD22.metaphlan.csv: taxonomy annotation from metaphlan4
LD847_HD22.qual.metabolomics.csv: a long format of qualitative metabolomics values. There is not unit associated with them.
LD847.ratios.quant.metabolomics.csv: primary to secondary bile acid ratios calculated in unit of mM.
taxumap_embedding.LD847.n375.csv: taxUmap coordinates
In vitro and mouse data_for repo_230713.xlsx: data for in vitro and mouse experiment. They are organized by tabs.
90day_survival_demographics_230518.csv: data used for survival analysis and Cox Proportional Harzard model for initial sample of each lactulose exposed patient.
qPCR_Calculations_MattO_220708 GF.xlsx: qPCR 16S copy number for Supp Fig 6, D.
MMF.16S.263_MattOdenwald.finalPhy_rdp.rds: phyloseq object for Supp Fig 6, D.
qual_compounds.csv: a list of all qualitative compounds to use in the heatmap
qual_heatmap_lookup.csv: a template for all qualitative compounds and their classes
mouse_consorita_phyloseq.rds: phyloseq object for Supp Fig 7
mouse_consortia_metab_quant.csv: quantitative metabolomic data for Supp Fig 7