├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── alpha.compare.R ├── meta.niceplot.R ├── meta.taxa.R ├── metatab.show.R ├── microbiomeage.R ├── pathway.compare.R ├── read.multi.R ├── taxa.compare.R ├── taxa.filter.R ├── taxa.mean.plot.R ├── taxa.meansdn.R └── taxcomtab.show.R ├── README.md ├── data ├── alphacom6.sex4.scaledg.rda ├── gtab.3stud.rda ├── metab.sex.rda ├── miage.rda ├── pathcom.ha6.rel.gamlss.sexg.rda ├── pathcom.rm6.rel.gamlss.sexg.rda ├── pathcom.unc6.rel.gamlss.sexg.rda ├── pathcom.usbmk6.rel.gamlss.sexg.rda ├── pathmetatab.zi.sexg.rda ├── rm4.sexs.rda ├── sam.rm.rda ├── studysum.rda ├── taxacom.6plus.sl5.rmg.rda ├── taxacom.dia.exbf2.zi.rmg.rda ├── taxacom.ha.sex.adjustbfage.rda ├── taxacom.rm.sex.adjustbfage.rda ├── taxacom6.rmg.rda ├── taxacom6.unc.sex.adjustedbfage.rda ├── taxacom6.zi.usbmk.sex.adjustbfage.rda └── taxtab.rm7.rda ├── inst └── extdata │ └── QIIME_outputs │ └── Bangladesh │ ├── Subramanian_et_al_mapping_file.txt │ ├── alpha_div_collated │ ├── PD_whole_tree.txt │ ├── chao1.txt │ ├── observed_species.txt │ └── shannon.txt │ ├── nature13421-s2.xlsx │ ├── picrust │ ├── metagenome_at_level1_edit.txt │ ├── metagenome_at_level2_edit.txt │ └── metagenome_at_level3_edit.txt │ └── tax_mapping7 │ ├── Subramanian_et_al_mapping_file_L2.txt │ ├── Subramanian_et_al_mapping_file_L3.txt │ ├── Subramanian_et_al_mapping_file_L4.txt │ ├── Subramanian_et_al_mapping_file_L5.txt │ ├── Subramanian_et_al_mapping_file_L6.txt │ └── Subramanian_et_al_mapping_file_L7.txt ├── man ├── alpha.compare.Rd ├── meta.niceplot.Rd ├── meta.taxa.Rd ├── metatab.show.Rd ├── microbiomeage.Rd ├── pathway.compare.Rd ├── read.multi.Rd ├── taxa.compare.Rd ├── taxa.filter.Rd ├── taxa.mean.plot.Rd ├── taxa.meansdn.Rd └── taxcomtab.show.Rd ├── metamicrobiomeR.Rproj ├── metamicrobiomeR.pdf └── metamicrobiomeR_Supplementary_file.html /.Rbuildignore: -------------------------------------------------------------------------------- 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