Files in SIAMCAT

Statistical Inference of Associations between Microbial Communities And host phenoTypes

.travis.yml

README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

data/meta_crc_zeller.RData

data/siamcat_example.RData

data/feat_crc_zeller.RData

R/check_associations.r R/import_packages.r R/read_label.r R/siamcat_class_accessors.R R/siamcat_class_helper_functions.R R/make_predictions.r R/check_confounders.r R/package_docs.R R/siamcat_class_constructor.R R/normalize_features.r R/evaluate_predictions.r R/validate_data.r R/siamcat_class_assignment_methods.R R/select_samples.r R/maaslinformat.R R/train_model.r R/lefseformat.R R/plm_utils.r R/create_data_split.r R/siamcat_all_class_definitions.R R/create_label.r R/summarize_features.R R/model_evaluation_plot.r R/add_meta_pred.r R/model_interpretation_plot.R R/filter_features.r R/data_docs.R

docs/index.html

docs/pkgdown.yml

docs/logo.png

docs/sitemap.xml

docs/docsearch.js

docs/docsearch.css

docs/authors.html

docs/pkgdown.js

docs/link.svg

docs/pkgdown.css

docs/articles/index.html

docs/articles/interpretation_plot.png

docs/articles/Slots_create.png

docs/articles/SIAMCAT_read-in.html

docs/articles/SIAMCAT_vignette.html

docs/articles/SIAMCAT_holdout.html

docs/articles/associations_plot.png

docs/articles/siamcat.png

docs/articles/allCr.png

docs/articles/SIAMCAT_vignette_files/figure-html/eval_plot-2.png

docs/articles/SIAMCAT_vignette_files/figure-html/eval_plot-1.png

docs/articles/SIAMCAT_holdout_files/figure-html/eval_plot_hidden-1.png

docs/reference/evaluate.predictions.html

docs/reference/model.interpretation.plot.html

docs/reference/read.label.html

docs/reference/accessSlot.html

docs/reference/siamcat-class.html

docs/reference/read.lefse.html

docs/reference/index.html

docs/reference/data_split-class.html

docs/reference/feature_weights-methods.html

docs/reference/summarize.features.html

docs/reference/assign-eval_data.html

docs/reference/filter.features.html

docs/reference/get.filt_feat.matrix.html

docs/reference/norm_feat-class.html

docs/reference/assign-associations.html

docs/reference/assign-filt_feat.html

docs/reference/meta-methods.html

docs/reference/model_list-class.html

docs/reference/filt_feat-methods.html

docs/reference/feat.crc.zeller.html

docs/reference/normalize.features.html

docs/reference/assign-orig_feat.html

docs/reference/siamcat_output.txt

docs/reference/data_split-methods.html

docs/reference/create.label.html

docs/reference/assoc_param-methods.html

docs/reference/label-class.html

docs/reference/associations-methods.html

docs/reference/physeq-methods.html

docs/reference/create.data.split.html

docs/reference/siamcat.html

docs/reference/orig_feat-methods.html

docs/reference/filter.label.html

docs/reference/add.meta.pred.html

docs/reference/models-methods.html

docs/reference/get.component.classes.html

docs/reference/norm_feat-methods.html

docs/reference/assign-data_split.html

docs/reference/assign-norm_feat.html

docs/reference/parse.label.header.html

docs/reference/feature_type-methods.html

docs/reference/meta.crc.zeller.html

docs/reference/get.norm_feat.matrix.html

docs/reference/select.samples.html

docs/reference/show-methods.html

docs/reference/get.orig_feat.matrix.html

docs/reference/eval_data-methods.html

docs/reference/siamcat.to.maaslin.html

docs/reference/check.confounders.html

docs/reference/associations-class.html

docs/reference/norm_params-methods.html

docs/reference/assign-physeq.html

docs/reference/assign-model_list.html

docs/reference/model_type-methods.html

docs/reference/train.model.html

docs/reference/check.associations.html

docs/reference/eval_data-class.html

docs/reference/label-methods.html

docs/reference/filt_feat-class.html

docs/reference/assign-label.html

docs/reference/filt_params-methods.html

docs/reference/pred_matrix-methods.html

docs/reference/validate.data.html

docs/reference/assign-pred_matrix.html

docs/reference/weight_matrix-methods.html

docs/reference/pred_matrix-class.html

docs/reference/SIAMCAT-package.html

docs/reference/make.predictions.html

docs/reference/siamcat.to.lefse.html

docs/reference/siamcat_example.html

docs/reference/assign-meta.html

docs/reference/model_list-methods.html

docs/reference/siamcat_output.pcl

docs/reference/model.evaluation.plot.html

docs/reference/figures/interpretation_plot.png

docs/reference/figures/logo.png

docs/reference/figures/embl_microbiome_tools_logo.png

docs/reference/figures/associations_plot.png

vignettes/eval_plot_holdout.png

vignettes/eval_plot.png

vignettes/SIAMCAT_vignette.Rmd

vignettes/interpretation_plot.png

vignettes/Slots_create.png

vignettes/SIAMCAT_holdout.Rmd

vignettes/associations_plot.png

vignettes/siamcat.png

vignettes/allCr.png

vignettes/SIAMCAT_read-in.Rmd man/show-methods.Rd man/assign-physeq.Rd man/get.orig_feat.matrix.Rd man/create.data.split.Rd man/orig_feat-methods.Rd man/model.interpretation.plot.Rd man/make.predictions.Rd man/assign-orig_feat.Rd man/evaluate.predictions.Rd man/filter.label.Rd man/get.component.classes.Rd man/check.associations.Rd man/get.norm_feat.matrix.Rd man/read.label.Rd man/associations-methods.Rd man/label-methods.Rd man/meta.crc.zeller.Rd man/siamcat.to.lefse.Rd man/get.filt_feat.matrix.Rd man/assign-associations.Rd man/train.model.Rd man/siamcat.Rd man/feature_type-methods.Rd man/assign-meta.Rd man/siamcat.to.maaslin.Rd man/model_type-methods.Rd man/filter.features.Rd man/check.confounders.Rd man/model.evaluation.plot.Rd man/assoc_param-methods.Rd man/normalize.features.Rd man/siamcat-class.Rd man/filt_params-methods.Rd man/physeq-methods.Rd man/models-methods.Rd man/assign-pred_matrix.Rd man/parse.label.header.Rd man/norm_feat-methods.Rd man/pred_matrix-methods.Rd man/filt_feat-methods.Rd man/norm_params-methods.Rd man/model_list-methods.Rd man/validate.data.Rd man/add.meta.pred.Rd man/eval_data-methods.Rd man/assign-model_list.Rd man/weight_matrix-methods.Rd man/feature_weights-methods.Rd man/meta-methods.Rd man/assign-norm_feat.Rd man/siamcat_example.Rd man/select.samples.Rd man/SIAMCAT-package.Rd man/assign-eval_data.Rd man/assign-label.Rd man/feat.crc.zeller.Rd man/summarize.features.Rd man/accessSlot.Rd man/data_split-methods.Rd man/create.label.Rd man/assign-data_split.Rd man/read.lefse.Rd man/assign-filt_feat.Rd

man/figures/interpretation_plot.png

man/figures/logo.png

man/figures/embl_microbiome_tools_logo.png

man/figures/associations_plot.png

inst/_pkgdown.yml

inst/NEWS

inst/CITATION

inst/doc/SIAMCAT_vignette.Rmd inst/doc/SIAMCAT_holdout.Rmd

inst/doc/SIAMCAT_read-in.html

inst/doc/SIAMCAT_holdout.R

inst/doc/SIAMCAT_vignette.html

inst/doc/SIAMCAT_read-in.R

inst/doc/SIAMCAT_holdout.html

inst/doc/SIAMCAT_read-in.Rmd inst/doc/SIAMCAT_vignette.R

inst/extdata/feat_crc_zeller_msb_mocat_specI.tsv

inst/extdata/num_metadata_crc_zeller_msb_mocat_specI.tsv

inst/extdata/label_crc_zeller_msb_mocat_specI.tsv

inst/extdata/LEfSe_crc_zeller_msb_mocat_specI.tsv

inst/extdata/maaslin.tsv

inst/extdata/maaslin.pcl

inst/templates/head.html

inst/templates/footer.html

SIAMCAT documentation built on Nov. 8, 2020, 5:14 p.m.