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

<p>*******************************************************************<br> MetaDrugs workflow<br> *******************************************************************</p> <p>Data analysis pipeline for investigating drug-host-microbiome relationships in cardiometabolic disease (MetaCardis cohort).</p> <p>For questions and requests, please contact:<br> Sofia K. Forslund (sofia.forslund@mdc-berlin.de)<br> and Till Birkner&nbsp; (till.birkner@mdc-berlin.de)</p> <p>*******************************************************************<br> Contents:<br> -------------------------------------------------------------------<br> Data files:<br> metadata.tar.gz - archived cohort metadata files*<br> input_features.tar.gz - archived preprocessed serum and urine metabolome and gut microbiome features<br> output_complete.tar.gz - archived example analysis output files for each of the input feature file<br> output_rerun.tar.gz - archived empty directory for generating test output files as described in this document<br> <br> *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.<br> -------------------------------------------------------------------<br> Text files:<br> archived in feature_names.tar.gz:<br> atcs_names - full names for atcs drug compounds<br> contrast_names - full names for disease comparison groups<br> file_names - brief description of the files in input_features folder<br> gmm_names - full names of GMM modules<br> kegg_names - full names of KEGG modules<br> ko_names - full names of KO modules<br> metadata_names - full names of metadata features<br> mOTU_names - species names for metagenomics data<br> taxon_names - taxon names for metagenomics data<br> -------------------------------------------------------------------<br> Scripts:<br> -------------------------------------------------------------------<br> runFrame.r - main wrapper script envoking the analysis pipeline<br> -------------------------------------------------------------------<br> runFrame_rel_comb.r - script calculating drug combination effects<br> runFrame_rel.r - script calculating dosage effects<br> testCombPresenceSeparate.r - testing of significant drug combination effects beyond single drug effects<br> testDosagePresenceSeparate.pl - testing of significant drug dosage effects beyond single drug effects<br> testDosagePresenceSeparateNegative.pl - testing of unique drug dosage effects beyond single drug effects<br> -------------------------------------------------------------------<br> prettifyResults_uncollapsed.pl - wrapper scripts to create and format a single analysis output file<br> makeTables.r - wrapper script to make excel tables with analysis results<br> -------------------------------------------------------------------<br> Example output file:<br> -------------------------------------------------------------------<br> output_all_formatted_noc_uncollapsed_complete.tsv - contains all disease-drug-host-microbiome feature analysis results in one place.<br> *******************************************************************</p>