Code accompanying the manuscript "The vaginal microbiome of pregnant people living with HIV on antiretroviral therapy in the Democratic Republic of Congo: A Pilot Study and Global Meta-analysis" 
Kimberley S Ndlovu
Ricardo R Pavan, PhD
contains the .RDS or .RDATA phyloseq files
• ps_congo_filt_spp is phyloseq of CVMB count data and taxa from the CQI-PMTCT (CONGO) samples that is filtered and agglomerated to species level
• ps_congo_filt_spp is phyloseq of CVMB count data and taxa from the CQI-PMTCT (CONGO) samples that is filtered, agglomerated to species level and transformed using robust centered log ratio
• ps_congo_picrust is a phyloseq of predicted metabolic pathways for the CQI-PMTCT (CONGO) samples
• ps_filt_spp_clr_zero is a phyloseq of CVMB count data and taxa from the intergated datasets that is filtered, zero sum ASVs removed, and transformed using centered log ratio
• ps_filt_spp_clr_zero_adj is a phyloseq of CVMB count data and taxa from the intergated datasets that is filtered, transformed using centered log ratio and batch adjusted
• ps_filt_spp_zero is a ps_filt_spp_clr_zero phyloseq of CVMB count data and taxa from the intergated datasets that is filtered and transformed using centered log ratio
• ps_meta_picrust is a phyloseq of predicted metabolic pathways for integrated datasets
• ps_raw_all is a phyloseq of raw count data for the integrated datasets
• DRC_CVMB_Figures_03.Rmd contains all scripts used to make the figures in the paper. Also includes analyses used to make the inputfiles for the figures
• functions_drc_cvmb.R functions used in the DRC_CVMB_Figures_03.Rmd
• dada2_congo_samples.R contains dada2 analyses for the CQI-PMTCT (CONGO) samples
• batch_adj_plots.Rmd contains batch adjustment scripts and figures for the integrated datasets
• contains all the input files for the code/DRC_CVMB_Figures_03.Rmd. Scripts to obtian the files are included in the same Rmd file.