Analysis code for: Microbial profiling of endometrioma and eutopic endometrium using 16S rRNA sequencing

Python code used for the analyses reported in the manuscript. Covers the paired analysis of eight patients, the calculation of R² for PERMANOVA, contamination screening, repeated rarefaction for the diversity analyses, summarization of the BLAST search of all 146 representative sequences, family-level composition, genus-level differential abundance with correction for multiple comparisons, and the sensitivity analysis for the dominant Escherichia lineage. Input data are the ASV table and representative sequences generated from the 16S rRNA gene sequencing data deposited under BioProject PRJDB40150. The random seed is fixed, so the reported values are reproducible.