Meta-analysis of 22,710 human metagenomes defines an index of oral to gut microbial introgression and associations with age, sex, BMI, and diseases

This entry contains the missing dataset from curatedMetagenomicData 3 needed to fully reproduce the analyses. The missing dataset, named HeQ_2017 refers to the following publication https://doi.org/10.1093/gigascience/gix050. Compared to the previous version, the only thing that changed is that oral enrichment data are now available in InputData/relative_abundances, and the compression algorithm changed. Like the previous version, the resource contains: InputData.tar.bz2 Folder with the data tables ready to be analyzed. The content of this folder should be copied into curatedMetagenomicDataAnalyses/cMD_paper_analyses before running all_command_lines.sh HeQ_2017.tar.gz The missing dataset in the format required to upload it into ExperimentHub HeQ_2017_merge_data_tables.sh The script used to generate the HeQ_2017_merged_tables folder and related content. md5sum hashes of the output tables are also included HeQ_2017_merge_with_cMD3_data_R.qmd A quarto document showing how to incorporate HeQ_2017 to a TreeSummarizedExperiment generated using curatedMetagenomicData in R HeQ_2017_merged_tables.tar.gz The folder containing the pre-merged MetaPhlAn3 and HUMAnN3 tables, the latter both as UniRef90 gene families (the default), and as Kegg Orthologs (KO) identifiers To reproduce the analyses: Clone curatedMetagenomicDataAnalyses locally `cd curatedMetagenomcDataAnalyses/cMD_paper_analyses` Download and extract InputData.tar.bz2 from this Zenodo entry Follow the instructions in the README.md you find there to run all analyses