The R Markdowns and R objets found here can be used to reproduce the analysis performed in the article titled "Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome"
Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd: R markdown script with all the code used to analyse alpha and beta diversity of the taxonomy and functional metagenomics data.
Metagenomics_Alpha_and_Beta_diversity_analysis.html: Knitted html document corresponding to Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd with the complete analysis of the metagenomic alpha and beta diversity for taxonomic and functional data.
Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd: R markdown script with all the code used to analyse differential abundance of the taxonomy and functional metagenomics data and differences in pathogenicity marker concentrations between women with and without T1D.
Metagenomics_DA_analysis_and_pathogenicity_markers.html: Knitted html document corresponding to Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd.
To view this file copy the complete address (https://github.com/PapenfussLab/RothSchulze_pregnancy-gut-microbiome-T1D/blob/master/Metagenomics_DA_analysis_and_pathogenicity_markers.html), go to https://htmlpreview.github.io/ paste and click enter.
Strain_level_phyloseq_object.RData: Contains the input for the markdown Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd and Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd in which taxonomic analyses where performed at the strain taxonomic level.
Species_level_phyloseq_object.RData: Contains the input for the markdown Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd and Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd in which taxonomic analyses where performed at the species taxonomic level.
Genus_level_phyloseq_object.RData: Contains the input for the markdown Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd and Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd in which taxonomic analyses where performed at the genus taxonomic level.
Family_level_phyloseq_object.RData: Contains the input for the markdown Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd and Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd in which taxonomic analyses where performed at the family taxonomic level.
Order_level_phyloseq_object.RData: Contains the input for the markdown Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd and Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd in which taxonomic analyses where performed at the order taxonomic level.
Phylum_level_phyloseq_object.RData: Contains the input for the markdown Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd and Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd in which taxonomic analyses where performed at the phylum taxonomic level.
Pathways_phyloseq_object.RData: Contains the input for the markdown Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd and Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd in which functional analyses where performed for pathways.
KEGG_Orthology_phyloseq_object.RData: Contains the input for the markdown Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd and Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd in which functional analyses where performed for Kegg orthology functional categories.
MetaCyc_reactions_phyloseq_object.RData: Contains the input for the markdown Metagenomics_Alpha_and_Beta_diversity_analysis.Rmd and Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd in which functional analyses where performed for MetaCyc reactions.
In addition, csv files containing concentrations of Calprotectin and I-FABP as well as a file containing the results from qPCR are included to be analysed within Markdown Metagenomics_DA_analysis_and_pathogenicity_markers.Rmd:
Calprotectin_measurements.csv
iFABP_measurements.csv
qPCR_data.csv