| SIAMCAT |
Man page
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| SIAMCAT-package |
Man page
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| accessSlot |
Man page
Source code
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| add.meta.pred |
Man page
Source code
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| analyse.binary.marker |
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| assign-data_split |
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| assign-eval_data |
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| assign-features |
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| assign-label |
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| assign-meta |
Man page
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| assign-model_list |
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| assign-norm_param |
Man page
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| assign-orig_feat |
Man page
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| assign-physeq |
Man page
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| assign-pred_matrix |
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| assign.fold |
Source code
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| associations.aucs.plot |
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| associations.bean.plot |
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| associations.box.plot |
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| associations.fcs.plot |
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| associations.labels.plot |
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| associations.margins.plot |
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| associations.pr.shift.plot |
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| associations.pvals.plot |
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| associations.quantile.box.plot |
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| associations.quantile.median.sub.plot |
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| associations.quantile.rect.plot |
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| associations.quantile.rect.sub.plot |
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| associations.quantiles.plot |
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| change.transparency |
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| check.associations |
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| check.associations.conf |
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| check.color.scheme |
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| check.confounders |
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| create.data.split |
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| create.label.from.metadata |
Man page
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| create.tints |
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| data_split |
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| data_split,ANY-method |
Man page
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| data_split,data_split-method |
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| data_split,list-method |
Man page
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| data_split-class |
Man page
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| data_split<- |
Man page
Man page
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| data_split<-,siamcat,data_split-method |
Man page
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| eval_data |
Man page
Man page
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| eval_data,ANY-method |
Man page
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| eval_data,list-method |
Man page
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| eval_data-class |
Man page
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| eval_data<- |
Man page
Man page
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| eval_data<-,siamcat,list-method |
Man page
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| evaluate.area.trapez |
Source code
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| evaluate.calc.aupr |
Source code
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| evaluate.classifier |
Source code
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| evaluate.get.pr |
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| evaluate.predictions |
Man page
Source code
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| feature.wise.anova.with.metadata |
Source code
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| features |
Man page
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| features,ANY-method |
Man page
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| features,otu_table-method |
Man page
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| features<- |
Man page
Man page
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| features<-,siamcat,otu_table-method |
Man page
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| filter.features |
Man page
Source code
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| filter.label |
Man page
Source code
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| get.component.classes |
Man page
Source code
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| get.features.matrix |
Man page
Source code
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| get.optimal.lambda.for.glmnet |
Source code
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| get.orig_feat.matrix |
Man page
Source code
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| get.parameters.from.param.set |
Source code
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| get.quantile.FC |
Source code
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| get.single.feat.AUC |
Source code
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| get.weights.matrix |
Source code
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| is.color |
Source code
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| is.component.class |
Source code
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| label |
Man page
Man page
Man page
Man page
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| label,ANY-method |
Man page
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| label,label-method |
Man page
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| label,list-method |
Man page
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| label-class |
Man page
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| label<- |
Man page
Man page
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| label<-,siamcat,label-method |
Man page
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| make.predictions |
Man page
Source code
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| marker.analysis.with.metadata |
Source code
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| measureAUPRC |
Source code
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| meta |
Man page
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| meta,ANY-method |
Man page
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| meta,sample_data-method |
Man page
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| meta<- |
Man page
Man page
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| meta<-,siamcat,sample_data-method |
Man page
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| model.evaluation.plot |
Man page
Source code
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| model.interpretation.feature.weights.plot |
Source code
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| model.interpretation.heatmap.plot |
Source code
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| model.interpretation.plot |
Man page
Source code
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| model.interpretation.pred.and.meta.plot |
Source code
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| model.interpretation.prepare.heatmap.fc |
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| model.interpretation.prepare.heatmap.zscore |
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| model.interpretation.proportion.of.weights.plot |
Source code
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| model.interpretation.select.features |
Source code
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| model_list |
Man page
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| model_list,ANY-method |
Man page
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| model_list,model_list-method |
Man page
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| model_list-class |
Man page
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| model_list<- |
Man page
Man page
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| model_list<-,siamcat,model_list-method |
Man page
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| model_type |
Man page
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| model_type,ANY-method |
Man page
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| model_type,model_list-method |
Man page
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| models |
Man page
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| models,ANY-method |
Man page
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| models,model_list-method |
Man page
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| norm_param |
Man page
Man page
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| norm_param,ANY-method |
Man page
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| norm_param,list-method |
Man page
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| norm_param-class |
Man page
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| norm_param<- |
Man page
Man page
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| norm_param<-,siamcat,list-method |
Man page
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| normalize.features |
Man page
Source code
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| orig_feat |
Man page
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| orig_feat,ANY-method |
Man page
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| orig_feat,orig_feat-method |
Man page
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| orig_feat,otu_table-method |
Man page
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| orig_feat-class |
Man page
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| orig_feat<- |
Man page
Man page
Man page
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| orig_feat<-,siamcat,orig_feat-method |
Man page
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| orig_feat<-,siamcat,otu_table-method |
Man page
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| parse.label.header |
Man page
Source code
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| physeq |
Man page
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| physeq,ANY-method |
Man page
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| physeq,phyloseq-method |
Man page
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| physeq<- |
Man page
Man page
Man page
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| physeq<-,siamcat,otu_table-method |
Man page
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| physeq<-,siamcat,phyloseq-method |
Man page
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| plot.percentage.of.features.plot |
Source code
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| pred_matrix |
Man page
Man page
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| pred_matrix,ANY-method |
Man page
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| pred_matrix,matrix-method |
Man page
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| pred_matrix-class |
Man page
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| pred_matrix<- |
Man page
Man page
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| pred_matrix<-,siamcat,matrix-method |
Man page
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| read.features |
Man page
Source code
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| read.labels |
Man page
Source code
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| read.lefse |
Man page
Source code
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| read.meta |
Man page
Source code
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| reset.features |
Man page
Source code
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| select.samples |
Man page
Source code
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| show,siamcat-method |
Man page
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| siamcat |
Man page
Source code
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| siamcat-class |
Man page
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| siamcat.to.lefse |
Man page
Source code
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| siamcat.to.maaslin |
Man page
Source code
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| siamcat_example |
Man page
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| single.pr.plot |
Source code
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| single.roc.plot |
Source code
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| train.model |
Man page
Source code
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| train.plm |
Source code
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| trim |
Source code
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| validate.data |
Man page
Source code
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