Data analysis pipeline for investigating drug-host-microbiome relationships in cardiometabolic disease (MetaCardis cohort).

******************************************************************* MetaDrugs workflow ******************************************************************* Data analysis pipeline for investigating drug-host-microbiome relationships in cardiometabolic disease (MetaCardis cohort). For questions and requests, please contact: Sofia K. Forslund ([email protected]) and Till Birkner ([email protected]) ******************************************************************* Contents: ------------------------------------------------------------------- Data files: metadata.tar.gz - archived cohort metadata files* input_features.tar.gz - archived preprocessed serum and urine metabolome and gut microbiome features output_complete.tar.gz - archived example analysis output files for each of the input feature file output_rerun.tar.gz - archived empty directory for generating test output files as described in this document *Please note: Due to conflicts with Danish Data Protection laws, metadata from the Danish subset of the cohort were removed in this repository. Please reach out for a potential case-by-case access request for access to the complete set of metadata. ------------------------------------------------------------------- Text files: archived in feature_names.tar.gz: atcs_names - full names for atcs drug compounds contrast_names - full names for disease comparison groups file_names - brief description of the files in input_features folder gmm_names - full names of GMM modules kegg_names - full names of KEGG modules ko_names - full names of KO modules metadata_names - full names of metadata features mOTU_names - species names for metagenomics data taxon_names - taxon names for metagenomics data ------------------------------------------------------------------- Scripts: ------------------------------------------------------------------- runFrame.r - main wrapper script envoking the analysis pipeline ------------------------------------------------------------------- runFrame_rel_comb.r - script calculating drug combination effects runFrame_rel.r - script calculating dosage effects testCombPresenceSeparate.r - testing of significant drug combination effects beyond single drug effects testDosagePresenceSeparate.pl - testing of significant drug dosage effects beyond single drug effects testDosagePresenceSeparateNegative.pl - testing of unique drug dosage effects beyond single drug effects ------------------------------------------------------------------- prettifyResults_uncollapsed.pl - wrapper scripts to create and format a single analysis output file makeTables.r - wrapper script to make excel tables with analysis results ------------------------------------------------------------------- Example output file: ------------------------------------------------------------------- output_all_formatted_noc_uncollapsed_complete.tsv - contains all disease-drug-host-microbiome feature analysis results in one place. *******************************************************************