├── .Rprofile ├── .github └── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── custom.md │ └── feature_request.md ├── .gitignore ├── LICENSE ├── README.md ├── app ├── Dockerfile ├── R │ ├── algorithms.R │ ├── data │ │ ├── example.biom │ │ └── spikes.fasta │ ├── fastq_utils.R │ ├── server.R │ ├── server │ │ ├── basic_server.R │ │ ├── confounding_server.R │ │ ├── differential_server.R │ │ ├── fastq_server.R │ │ ├── filtering_server.R │ │ ├── functional_server.R │ │ ├── ml_server.R │ │ ├── multiomics_server.R │ │ ├── network_server.R │ │ ├── phylogenetic_server.R │ │ ├── texts_server.R │ │ ├── upload_dada2_server.R │ │ ├── upload_lotus2_server.R │ │ ├── upload_msd_server.R │ │ ├── upload_multiomics_server.R │ │ ├── upload_otu_server.R │ │ └── upload_sample_server.R │ ├── src │ │ ├── graph.cpp │ │ ├── graph.hpp │ │ ├── rm_spikes.py │ │ ├── spikes_normalizer.py │ │ └── topological_sorting.cpp │ ├── testdata │ │ ├── OTU_table.tab │ │ ├── metabolomics_expression.tsv │ │ ├── metafile.tab │ │ ├── picrust2 │ │ │ ├── ec_pred_metagenome_unstrat_descrip.tsv.gz │ │ │ ├── ko_pred_metagenome_unstrat_descrip.tsv.gz │ │ │ ├── marker_predicted_and_nsti.tsv.gz │ │ │ └── path_abun_unstrat_descrip.tsv.gz │ │ ├── seqs.fasta │ │ └── tree.tre │ ├── texts.R │ ├── ui.R │ ├── utils.R │ └── www │ │ ├── Logo.png │ │ ├── biomedbigdata_logo_wide_TUM.png │ │ ├── daisybio_logo_tum.png │ │ ├── horizon_logo.png │ │ ├── logo2.png │ │ ├── namco_workflow_final.png │ │ └── tum_logo.png ├── conda_env.yml ├── renv.lock ├── shiny-server.conf └── shiny-server.sh ├── dependencies.R ├── docker-compose.yml ├── namco.Rproj ├── nginx └── nginx.conf ├── renv ├── .gitignore ├── activate.R └── settings.dcf └── shinyproxy ├── Dockerfile └── application.yml /.Rprofile: -------------------------------------------------------------------------------- 1 | source("renv/activate.R") 2 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: 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