Files in KonradZych/SIAMCAT

Statistical Inference of Associations between Microbial Communities And host phenoTypes

.gitignore

DESCRIPTION

NAMESPACE

R/add_meta_pred.r R/check_associations.r R/check_associations_conf.r R/check_confounders.r R/create_data_split.r R/create_label_from_metadata.r R/data_docs.R R/evaluate_predictions.r R/filter_features.r R/import_packages.r R/io_utils.r R/lefseformat.R R/maaslinformat.R R/make_predictions.r R/model_evaluation_plot.r R/model_interpretation_plot.R R/normalize_features.r R/package_docs.R R/plm_utils.r R/select_samples.r R/siamcat_all_class_definitions.R R/siamcat_class_accessors.R R/siamcat_class_assignment_methods.R R/siamcat_class_constructor.R R/siamcat_class_helper_functions.R R/train_model.r R/validate_data.r README.md

data/siamcat_example.RData

docs/LICENSE.html

docs/articles/SIAMCAT_vignette.html

docs/articles/SIAMCAT_vignette_files/figure-html/unnamed-chunk-17-1.png

docs/articles/SIAMCAT_vignette_files/figure-html/unnamed-chunk-19-1.png

docs/articles/SIAMCAT_vignette_files/figure-html/unnamed-chunk-20-1.png

docs/articles/SIAMCAT_vignette_files/figure-html/unnamed-chunk-22-1.png

docs/articles/SIAMCAT_vignette_files/figure-html/unnamed-chunk-8-1.png

docs/articles/SIAMCAT_vignette_files/figure-html/unnamed-chunk-9-1.png

docs/articles/index.html

docs/authors.html

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/logo.png

docs/pkgdown.css

docs/pkgdown.js

docs/reference/SIAMCAT-package.html

docs/reference/accessSlot.html

docs/reference/add.meta.pred.html

docs/reference/appendDirName.html

docs/reference/assign-data_split.html

docs/reference/assign-eval_data.html

docs/reference/assign-features.html

docs/reference/assign-label.html

docs/reference/assign-meta.html

docs/reference/assign-model_list.html

docs/reference/assign-norm_param.html

docs/reference/assign-orig_feat.html

docs/reference/assign-physeq.html

docs/reference/assign-pred_matrix.html

docs/reference/assign.fold.html

docs/reference/check.associations.html

docs/reference/check.confounders.html

docs/reference/confounder.check.html

docs/reference/create.data.split.html

docs/reference/create.label.from.metadata.html

docs/reference/create.label.html

docs/reference/data.splitter.html

docs/reference/dataSplit-class.html

docs/reference/data_split-class.html

docs/reference/data_split-methods.html

docs/reference/eval,pdf

docs/reference/eval.predictions.html

docs/reference/eval.result.html

docs/reference/eval_data-class.html

docs/reference/eval_data-methods.html

docs/reference/evaluate.predictions.html

docs/reference/evaluation.model.plot-1.png

docs/reference/evaluation.model.plot-2.png

docs/reference/evaluation.model.plot-3.png

docs/reference/evaluation.model.plot-4.png

docs/reference/evaluation.model.plot-5.png

docs/reference/evaluation.model.plot-6.png

docs/reference/evaluation.model.plot-7.png

docs/reference/evaluation.model.plot-8.png

docs/reference/evaluation.model.plot.html

docs/reference/features-methods.html

docs/reference/figures/logo.png

docs/reference/filter.feat.html

docs/reference/filter.features.html

docs/reference/filter.label.html

docs/reference/get.component.classes.html

docs/reference/get.eval_data.html

docs/reference/get.features.html

docs/reference/get.features.matrix.html

docs/reference/get.label.html

docs/reference/get.label.info.html

docs/reference/get.label.label.html

docs/reference/get.label.list.html

docs/reference/get.model.type.html

docs/reference/get.model_list.html

docs/reference/get.models.html

docs/reference/get.orig_feat.matrix.html

docs/reference/get.phyloseq.html

docs/reference/get.pred_matrix.html

docs/reference/index.html

docs/reference/interpretion,pdf

docs/reference/interpretor.model.plot.html

docs/reference/label-class.html

docs/reference/label-methods.html

docs/reference/make.predictions.html

docs/reference/meta-methods.html

docs/reference/model.evaluation.plot.html

docs/reference/model.interpretation.plot.html

docs/reference/modelList-class.html

docs/reference/model_list-class.html

docs/reference/model_list-methods.html

docs/reference/model_type-methods.html

docs/reference/models-methods.html

docs/reference/norm_param-methods.html

docs/reference/normalize.feat.html

docs/reference/normalize.features.html

docs/reference/orig_feat-methods.html

docs/reference/parse.label.header.html

docs/reference/physeq-methods.html

docs/reference/plm.predictor.html

docs/reference/plm.trainer.html

docs/reference/pred_matrix-class.html

docs/reference/pred_matrix-methods.html

docs/reference/read.features.html

docs/reference/read.labels.html

docs/reference/read.meta.html

docs/reference/reset.features.html

docs/reference/select.samples.html

docs/reference/show-methods.html

docs/reference/siamcat-class.html

docs/reference/siamcat.html

docs/reference/siamcat_example.html

docs/reference/train.model.html

docs/reference/validate.data.html

docs/tidyverse.css

inst/CITATION

inst/NEWS

inst/extdata/LEfSe_crc_zeller_msb_mocat_specI.tsv

inst/extdata/feat_crc_zeller_msb_mocat_specI.tsv

inst/extdata/label_crc_zeller_msb_mocat_specI.tsv

inst/extdata/maaslin.pcl

inst/extdata/maaslin.tsv

inst/extdata/num_metadata_crc_zeller_msb_mocat_specI.tsv

man/SIAMCAT-package.Rd man/accessSlot.Rd man/add.meta.pred.Rd man/assign-data_split.Rd man/assign-eval_data.Rd man/assign-features.Rd man/assign-label.Rd man/assign-meta.Rd man/assign-model_list.Rd man/assign-norm_param.Rd man/assign-orig_feat.Rd man/assign-physeq.Rd man/assign-pred_matrix.Rd man/check.associations.Rd man/check.confounders.Rd man/create.data.split.Rd man/create.label.from.metadata.Rd man/data_split-class.Rd man/data_split-methods.Rd man/eval_data-class.Rd man/eval_data-methods.Rd man/evaluate.predictions.Rd man/features-methods.Rd

man/figures/logo.png

man/filter.features.Rd man/filter.label.Rd man/get.component.classes.Rd man/get.features.matrix.Rd man/get.orig_feat.matrix.Rd man/label-class.Rd man/label-methods.Rd man/make.predictions.Rd man/meta-methods.Rd man/model.evaluation.plot.Rd man/model.interpretation.plot.Rd man/model_list-class.Rd man/model_list-methods.Rd man/model_type-methods.Rd man/models-methods.Rd man/norm_param-class.Rd man/norm_param-methods.Rd man/normalize.features.Rd man/orig_feat-class.Rd man/orig_feat-methods.Rd man/parse.label.header.Rd man/physeq-methods.Rd man/pred_matrix-class.Rd man/pred_matrix-methods.Rd man/read.features.Rd man/read.labels.Rd man/read.lefse.Rd man/read.meta.Rd man/reset.features.Rd man/select.samples.Rd man/show-methods.Rd man/siamcat-class.Rd man/siamcat.Rd man/siamcat.to.lefse.Rd man/siamcat.to.maaslin.Rd man/siamcat_example.Rd man/train.model.Rd man/validate.data.Rd vignettes/SIAMCAT_read-in.Rmd vignettes/SIAMCAT_vignette.Rmd

vignettes/Slots_create.png

vignettes/allCr.png

vignettes/association_plot.png

vignettes/interpretation_plot.png

vignettes/siamcat.png

KonradZych/SIAMCAT documentation built on May 17, 2019, 6:20 p.m.