├── .Rhistory ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── .Rhistory └── MLP.R ├── README.md ├── assets └── MLP_logo2.png ├── example_code.R ├── inst └── extdata │ ├── 16S_rRNA │ └── model.16S_rRNA.rds │ ├── galaxy │ ├── model.metaphlan3.rds │ ├── model.metaphlan3.tr.rds │ ├── model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.rds │ ├── model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.tr.rds │ ├── model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.rds │ ├── model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.tr.rds │ ├── model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.rds │ ├── model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.tr.rds │ ├── model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.rds │ ├── model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.tr.rds │ ├── model.motus25.rds │ ├── model.motus25.tr.rds │ ├── model.motus3.rds │ └── model.motus3.tr.rds │ └── metacardis │ ├── model.metaphlan3.rds │ ├── model.metaphlan3.tr.rds │ ├── model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.rds │ ├── model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.tr.rds │ ├── model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.rds │ ├── model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.tr.rds │ ├── model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.rds │ ├── model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.tr.rds │ ├── model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.rds │ ├── model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.tr.rds │ ├── model.motus25.rds │ ├── model.motus25.tr.rds │ ├── model.motus3.rds │ └── model.motus3.tr.rds ├── man └── MLP.Rd └── test_data ├── Franzosa_2018_IBD.metadata.tsv ├── Franzosa_2018_IBD.metaphlan3.tsv ├── Franzosa_2018_IBD.metaphlan4.tsv ├── Franzosa_2018_IBD.motus25.tsv ├── Franzosa_2018_IBD.motus3.tsv └── Vandeputte_2017_16S.tsv /.Rhistory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/.Rhistory -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/.Rhistory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/R/.Rhistory -------------------------------------------------------------------------------- /R/MLP.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/R/MLP.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/README.md -------------------------------------------------------------------------------- /assets/MLP_logo2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/assets/MLP_logo2.png -------------------------------------------------------------------------------- /example_code.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/example_code.R -------------------------------------------------------------------------------- /inst/extdata/16S_rRNA/model.16S_rRNA.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/16S_rRNA/model.16S_rRNA.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan3.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan3.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan3.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan3.tr.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.tr.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.tr.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.tr.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.tr.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.motus25.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.motus25.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.motus25.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.motus25.tr.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.motus3.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.motus3.rds -------------------------------------------------------------------------------- /inst/extdata/galaxy/model.motus3.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/galaxy/model.motus3.tr.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan3.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan3.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan3.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan3.tr.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan4.mpa_vJan21_CHOCOPhlAnSGB_202103.tr.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan4.mpa_vJan25_CHOCOPhlAnSGB_202503.tr.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202307.tr.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.metaphlan4.mpa_vJun23_CHOCOPhlAnSGB_202403.tr.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.motus25.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.motus25.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.motus25.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.motus25.tr.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.motus3.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.motus3.rds -------------------------------------------------------------------------------- /inst/extdata/metacardis/model.motus3.tr.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/inst/extdata/metacardis/model.motus3.tr.rds -------------------------------------------------------------------------------- /man/MLP.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/man/MLP.Rd -------------------------------------------------------------------------------- /test_data/Franzosa_2018_IBD.metadata.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/test_data/Franzosa_2018_IBD.metadata.tsv -------------------------------------------------------------------------------- /test_data/Franzosa_2018_IBD.metaphlan3.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/test_data/Franzosa_2018_IBD.metaphlan3.tsv -------------------------------------------------------------------------------- /test_data/Franzosa_2018_IBD.metaphlan4.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/test_data/Franzosa_2018_IBD.metaphlan4.tsv -------------------------------------------------------------------------------- /test_data/Franzosa_2018_IBD.motus25.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/test_data/Franzosa_2018_IBD.motus25.tsv -------------------------------------------------------------------------------- /test_data/Franzosa_2018_IBD.motus3.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/test_data/Franzosa_2018_IBD.motus3.tsv -------------------------------------------------------------------------------- /test_data/Vandeputte_2017_16S.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/grp-bork/microbial_load_predictor/HEAD/test_data/Vandeputte_2017_16S.tsv --------------------------------------------------------------------------------