- Faecal microbiota of schoolchildren is associated with nutritional status, micronutrient 2 status and markers of inflammation
- baseline_top_taxa.R is the R-script used to plot the top taxa at the baseline.
- bray_curtis_PCoA_plot.R is the R-script used to generate PCoA plot of the bray_curtis at the Baseline and Endline.
- core_microbiome_final.R is the R-script used to calculate the core microbiota at the baseline
- forward_dada2.R is the R-script used to process the raw sequence.
- __config.R is a configuration file that must be located in the same working directory as the forward_dada2.R script.
- glm_lefse.R implements a linear mixed model on microbial features identified as significant by Linear discriminant analysis Effect Size (LEfSe).
- linear_model_alphadiversity.R is a linear mixed model on alpha diversity metrics at the baseline.
- Maaslin2.R is the R-script used to generate the linear mixed models.
- phyloseq_final.R is the R-script used to generate the phyloseq object and prilimary processing.
- QIIME2_alpha_beta_diversity_baseline folder contains command used to generate alpha and beta diversity differences at the baseline, metadata, feature-table, tree and README file.
- QIIME2_longitudinal_alpha_diversity folder contains command used to generate longitudinal differences in alpha diversity, metadata, feature-table, tree and README file.
- QIIME2_longitudinal_beta_diversity folder contains command used to generate longitudinal differences in beta diversity, metadata, feature-table, tree and README file.
- test_data folder contains test data (13-sample (.fastq file)and metadata (.xlsx)).
- prevabun_tree0_rooted.rds is the final phyloseq object generated using phyloseq_final.R script
- Modify the "dbs" value in the _"_config.R" file to ensure the forward_dad2.R script runs properly
- This assume you have downloaded the [silva_nr99_v138.1_wSpecies_train_set.fa.gz] (https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz?download=1) file and placed it in a folder named "database" within your working directory.
- dbs = list("16S" = "~/your_working_directory/database/silva_nr99_v138.1_wSpecies_train_set.fa.gz")