├── .gitignore ├── LICENSE ├── README.md ├── _config.yml ├── add-datasets-readme.md ├── datasets ├── bacteremia │ ├── gg │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ └── task.txt ├── bushman_cafe │ ├── gg │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ └── task.txt ├── cho │ ├── gg │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-cecal.txt │ ├── mapping-fecal.txt │ ├── mapping-orig.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── task-control-ct-cecal.txt │ ├── task-control-ct-fecal.txt │ ├── task-penicillin-vancomycin-cecal.txt │ └── task-penicillin-vancomycin-fecal.txt ├── claesson │ ├── gg │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── mapping-suppl.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ └── task.txt ├── david │ ├── gg │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ └── task.txt ├── gevers │ ├── gg │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── mapping-suppl.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── task-ileum.txt │ ├── task-pcdai-ileum.txt │ ├── task-pcdai-rectum.txt │ └── task-rectum.txt ├── hmp │ ├── gg │ │ ├── otutable.txt.zip │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── task-gastro-oral.txt │ ├── task-sex.txt │ ├── task-stool-tongue-paired.txt │ └── task-sub-supragingivalplaque-paired.txt ├── karlsson │ ├── mapping-orig.txt │ ├── otutable.txt │ ├── task-impaired-diabetes.txt │ ├── task-normal-diabetes.txt │ └── taxatable.txt ├── kostic │ ├── gg │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── mapping.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ └── task.txt ├── qin2012 │ ├── mapping-orig.txt │ ├── otutable.txt │ ├── task-healthy-diabetes.txt │ └── taxatable.txt ├── qin2014 │ ├── mapping-orig.txt │ ├── otutable.txt │ ├── task-healthy-cirrhosis.txt │ └── taxatable.txt ├── ravel │ ├── gg │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── task-black-hispanic.txt │ ├── task-nugent-category.txt │ ├── task-nugent-score.txt │ ├── task-ph.txt │ └── task-white-black.txt ├── sokol │ ├── gg │ │ ├── otutable.biom │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── mapping-uc-cd-healthy.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── task-healthy-cd.txt │ └── task-healthy-uc.txt ├── turnbaugh │ ├── gg │ │ ├── otutable.txt │ │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── refseq │ │ ├── otutable.txt │ │ └── taxatable.txt │ └── task-obese-lean-all.txt └── yatsunenko │ ├── gg │ ├── otutable.txt │ └── taxatable.txt │ ├── mapping-orig.txt │ ├── refseq │ ├── otutable.txt │ └── taxatable.txt │ ├── task-baby-age.txt │ ├── task-malawi-venezuela.txt │ ├── task-sex.txt │ └── task-usa-malawi.txt ├── docs ├── bacteremia.md ├── bacteremia_nobacteremia.md ├── bushman_cafe.md ├── bushman_diet.md ├── cho.md ├── cho_control_ct_cecal.md ├── cho_control_ct_fecal.md ├── cho_pen_vanc_cecal.md ├── cho_pen_vanc_fecal.md ├── claesson.md ├── claesson_elderly.md ├── david.md ├── david_animal_plant.md ├── gevers.md ├── gevers_control_cd_ileum.md ├── gevers_control_cd_rectum.md ├── gevers_pcdai_ileum.md ├── gevers_pcdai_rectum.md ├── hmp.md ├── hmp_gastro_oral.md ├── hmp_male_female.md ├── hmp_stool_tongue.md ├── hmp_sub_supra.md ├── karlsson.md ├── karlsson_impaired_diabetes.md ├── karlsson_normal_diabetes.md ├── kostic.md ├── kostic_healthy_tumor.md ├── qin2012.md ├── qin2014.md ├── qin_healthy_cirrhosis.md ├── qin_healthy_diabetes.md ├── ravel.md ├── ravel_black_hispanic.md ├── ravel_nugent_category.md ├── ravel_nugent_score.md ├── ravel_ph.md ├── ravel_white_black.md ├── sokol.md ├── sokol_healthy_cd.md ├── sokol_healthy_uc.md ├── turnbaugh_lean_obese_all.md ├── turnbaugh_twins.md ├── yatsunenko.md ├── yatsunenko_infantage.md ├── yatsunenko_malawi_venezuela.md ├── yatsunenko_male_female.md └── yatsunenko_us_malawi.md ├── example ├── README.md ├── lib │ ├── collapse-features.r │ ├── cross.validation.caret.r │ ├── cross.validation.stats.r │ ├── plot.rocs.r │ └── run.cv.datasets.r ├── output │ ├── db.rocs.pdf │ ├── legend1.db.rocs.pdf │ ├── legend1.ml.rocs.pdf │ ├── legend2.db.rocs.pdf │ ├── legend2.ml.rocs.pdf │ └── ml.rocs.pdf └── run.r └── web ├── .editorconfig ├── .idea ├── misc.xml ├── modules.xml ├── web.iml └── workspace.xml └── data ├── dataset_metadata.xlsx ├── datasets.txt └── tasks.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/knights-lab/MLRepo/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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