SIAMCAT
Statistical Inference of Associations between Microbial Communities And host phenoTypes

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199
Source code
30
Man pages
63
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SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes
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API for SIAMCAT
Statistical Inference of Associations between Microbial Communities And host phenoTypes

Global functions
SIAMCAT Man page
SIAMCAT-package Man page
accessSlot Man page Source code
add.meta.pred Man page Source code
analyse.binary.marker Source code
assign-associations Man page
assign-data_split Man page
assign-eval_data Man page
assign-filt_feat Man page
assign-label Man page
assign-meta Man page
assign-model_list Man page
assign-norm_feat Man page
assign-orig_feat Man page
assign-physeq Man page
assign-pred_matrix Man page
assign.fold Source code
assoc_param Man page
assoc_param,siamcat-method Man page
assoc_param_param Man page
associations Man page
associations,siamcat-method Man page
associations.aucs.plot Source code
associations.bean.plot Source code
associations.box.plot Source code
associations.fcs.plot Source code
associations.labels.plot Source code
associations.margins.plot Source code
associations.pr.shift.plot Source code
associations.pvals.plot Source code
associations.quantile.box.plot Source code
associations.quantile.median.sub.plot Source code
associations.quantile.rect.plot Source code
associations.quantile.rect.sub.plot Source code
associations.quantiles.plot Source code
associations<- Man page
associations<-,siamcat,list-method Man page
change.transparency Source code
check.assoc Source code
check.associations Man page Source code
check.color.scheme Source code
check.confounders Man page Source code
check.data.split Source code
check.eval.data Source code
check.filt.feat Source code
check.label Source code
check.model.list Source code
check.norm.feat Source code
check.siamcat Source code
confounders.build.glms Source code
confounders.corrplot Source code
confounders.descriptive.plots Source code
confounders.glm.auroc.plot Source code
confounders.glm.reg.coef.plot Source code
confounders.glm.reg.pval.plot Source code
create.data.split Man page Source code
create.label Man page Source code
create.tints Source code
data_split Man page
data_split,siamcat-method Man page
data_split<- Man page
data_split<-,siamcat,list-method Man page
eval_data Man page
eval_data,siamcat-method Man page
eval_data<- Man page
eval_data<-,siamcat,list-method Man page
evaluate.area.trapez Source code
evaluate.calc.aupr Source code
evaluate.classifier Source code
evaluate.get.pr Source code
evaluate.predictions Man page Source code
factorize.bmi Source code
factorize.metadata Source code
feat.crc.zeller Man page
feature_type Man page
feature_type,siamcat-method Man page
feature_weights Man page
feature_weights,siamcat-method Man page
filt_feat Man page
filt_feat,siamcat-method Man page
filt_feat<- Man page
filt_feat<-,siamcat,list-method Man page
filt_params Man page
filt_params,siamcat-method Man page
filter.features Man page Source code
filter.label Man page Source code
get.component.classes Man page Source code
get.filt_feat.matrix Man page Source code
get.names Source code
get.norm_feat.matrix Man page Source code
get.optimal.lambda.for.glmnet Source code
get.orig_feat.matrix Man page Source code
get.parameters.from.param.set Source code
get.plotting.idx Source code
get.quantile.FC Source code
get.single.feat.AUC Source code
is.color Source code
is.component.class Source code
label Man page
label,siamcat-method Man page
label<- Man page
label<-,siamcat,list-method Man page
make.predictions Man page Source code
measureAUPRC Source code
meta Man page
meta,sample_data-method Man page
meta,siamcat-method Man page
meta.crc.zeller Man page
meta<- Man page
meta<-,siamcat,sample_data-method Man page
model.evaluation.plot Man page Source code
model.interpretation.feature.weights.plot Source code
model.interpretation.heatmap.plot Source code
model.interpretation.plot Man page Source code
model.interpretation.pred.and.meta.plot Source code
model.interpretation.prepare.heatmap.fc Source code
model.interpretation.prepare.heatmap.zscore Source code
model.interpretation.proportion.of.weights.plot Source code
model.interpretation.select.features Source code
model_list Man page
model_list,siamcat-method Man page
model_list<- Man page
model_list<-,siamcat,list-method Man page
model_type Man page
model_type,siamcat-method Man page
models Man page
models,siamcat-method Man page
norm_feat Man page
norm_feat,siamcat-method Man page
norm_feat<- Man page
norm_feat<-,siamcat,list-method Man page
norm_params Man page
norm_params,siamcat-method Man page
normalize.features Man page Source code
orig_feat Man page
orig_feat,otu_table-method Man page
orig_feat,siamcat-method Man page
orig_feat<- Man page
orig_feat<-,siamcat,otu_table-method Man page
parse.label.header Man page Source code
physeq Man page
physeq,ANY-method Man page
physeq,phyloseq-method Man page
physeq<- Man page
physeq<-,siamcat,phyloseq-method Man page
plot.percentage.of.features.plot Source code
pred_matrix Man page
pred_matrix,siamcat-method Man page
pred_matrix<- Man page
pred_matrix<-,siamcat,matrix-method Man page
read.label Man page Source code
read.lefse Man page Source code
select.samples Man page Source code
show,siamcat-method Man page
siamcat Man page Source code
siamcat-class Man page
siamcat.to.lefse Man page Source code
siamcat.to.maaslin Man page Source code
siamcat_example Man page
single.pr.plot Source code
single.roc.plot Source code
summarize.features Man page Source code
train.model Man page Source code
train.plm Source code
trim Source code
validate.data Man page Source code
validate.features Source code
validate.label Source code
validate.metadata Source code
variance.plots Source code
weight_matrix Man page
weight_matrix,siamcat-method Man page
SIAMCAT documentation built on Nov. 8, 2020, 5:14 p.m.

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