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