Metadata for all samples, custom code and input tables for our manuscript "Archaea influence composition of endoscopically visible ileocolonic biofilms"
16S rRNA gene amplicon sequencing data was deposited under the BioProject accession number PRJNA644520 (cohort 1) and PRJNA1100194 (cohort 2).
- Beta diversity and group comparisons in cohort 1 have been performed using Rhea scripts (https://github.com/Lagkouvardos/Rhea).
- Subgroup analysis in cohort 1 has been done with DSEq2.
- Additionally a machine learning model using qiime2 sample classifier plugin, according to (https://docs.qiime2.org/2024.2/tutorials/sample-classifier/).
- Linear models were generated using MaAslin2 (https://github.com/biobakery/Maaslin2)