├── .gitignore ├── 16S18S ├── css_transform.R ├── hellinger_transform.R ├── import_16S.R ├── import_taxonomy.R ├── phyloseq_construct.R └── tss_transform.R ├── LICENSE ├── README.md ├── contextualData └── import_contextual_data.R ├── doc └── handbook │ ├── OSD_Handbook_2014-06.pdf │ ├── OSD_Handbook_2015-06.pdf │ └── OSD_Handbook_2016-04.pdf ├── docs ├── Gemfile ├── Gemfile.lock ├── _config.yml ├── _data │ └── navigation.yaml ├── _includes │ ├── edit-link.html │ └── navigation.html ├── _layouts │ └── default.html ├── assets │ └── css │ │ └── style.scss ├── data │ ├── 2014 │ │ └── index.md │ ├── 2015 │ │ └── index.md │ └── 2016 │ │ └── index.md ├── docker-compose.yaml ├── index.md ├── page-configuration.md ├── pre-processing.md └── super.md ├── emgData ├── README.md ├── import_ipr.R ├── ipr_css_transform.R ├── ipr_hellinger_transform.R └── ipr_tss_transform.R ├── images └── osd-pre-processsing-activity-diagram-2014.png ├── otuTables ├── README.md ├── create_otu_table.py └── 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