This readme will describe each RMD file and their purpose. The user may execute the code in the same order as this file.
---- functions.R input
- functions useful for all scripts
- functions for processinng phyloseq objects
output
- curated_v3_otu_tax.rda : the CMD raw data.
---- Projet-1.Rmd input curated_v3_otu_tax.rda
- filtering the CMD data
- basic exploratory/statistical analyses
output study_after_QC.rda
- study_after_QC.rda : CMD filtered data.
---- Heatmaps.Rmd input curated_v3_otu_tax.rda
- heatmaps accross host factors
output
---- run_spiec_easi_analyse.Rmd input study_after_QC.rda
- Bifidobacterium network analyses
output phy_curated_data_after_QC.rda
phy_deseq_analysis_150
- phy_curated_data_after_QC.rda : CMD filtered data (phyloseq objects)
- phy_deseq_analysis_150 : CMD filtered data with 150 most abundant otu (phyloseq objects)
---- DMM_clustering.Rmd input study_after_QC.rda phy_curated_data_after_QC.rda
- DMM clustering and all descriptive clusters
- when running, choose whole curated for origin CMD bifidotypes
output enterotype_DMM
all files created in DMM_files folder
- enterotype_DMM : contaning the CMD bifidotypes
---- differential_analysis.Rmd input phy_deseq_analysis_150 enterotype_DMM
- DMM clustering and all descriptive clusters
output
- data-raw : alias of data-raw folder
---- MAGS_analysis.Rmd input all input are located in data-raw
- MAGs analyses :
- inter/intra species heatmaps
output
---- bif_rda_analysis.Rmd input inputs are located in data-raw enterotype_DMM
- MASH analyses with bifidotypes X 15 phage eggnogs associated
output
---- eggnogs_MAGS.Rmd input are located in data-raw curated_v3_otu_tax.rda enterotype_DMM
- all the Chisquare analyses
- interspecies and with unhealthy/healthy bifidotypes
output all the association files
- test : contains IGC.egg5.0.tsv
- IGC.eggNOG_v5.0.tsv : MSP EggNOG composition
- association_eggnogs_metadata_grp_healthy.csv : eggnog X bifidotypes association
- association_eggnogs_metadata_age_category.csv : eggnog X age association
- association_eggnogs_metadata_westernized.csv : eggnog X westernized association
- association_species_species.csv : eggnog species X eggnog other species association
MI_metadata_extraction.xlsx : metadata MI sample_metadata_msp.xlsx : metadata MI
---- MSP_analysis.Rmd input are located in data-raw IGC.eggNOG_v5.0.tsv curated_v3_otu_tax.rda DMM_files/best_fit_DMM_6clusters MI_metadata_extraction.xlsx sample_metadata_msp.xlsx
- predict the bifidotypes
- of milieu interieur based on CMD 6 clusters
- Shannon diversity
output
---- DMM_MSP.Rmd input are located in data-raw IGC.eggNOG_v5.0.tsv curated_v3_otu_tax.rda DMM_files/best_fit_DMM_6clusters association_eggnogs_metadata_grp_healthy.csv MI_metadata_extraction.xlsx sample_metadata_msp.xlsx
- de novo DMM clustering on DMM
- explorative analyses with diet factors
- diversity, age, CRP, nutritional factors
output
---- MI_MSP_exploration.Rmd input are located in data-raw IGC.eggNOG_v5.0.tsv curated_v3_otu_tax.rda DMM_files/best_fit_DMM_6clusters association_eggnogs_metadata_grp_healthy.csv
- predict the bifidotypes
- of milieu interieur based on CMD 6 clusters
- test the prevalence of the 4 phage eggnogs
output df_healthy_msp.csv
- df_healthy_msp.csv : heatmap MSP X Subjects : contains the counts of 4 phage eggnogs (B. bifidum)
---- MI_MSP_exploration_simplified.Rmd input are located in data-raw sample_metadata_msp.xlsx MI_metadata_extraction.xlsx df_healthy_msp.csv
- predict the bifidotypes
- of milieu interieur based on CMD 6 clusters
- test the prevalence of the 4 phage eggnogs
output