API for computational-metabolomics/structToolbox
Data processing & analysis tools for Metabolomics and other omics

Global functions
ANOVA Man page Source code
AUC Man page Source code
DFA Man page Source code
DatasetExperiment_boxplot Man page Source code
DatasetExperiment_dist Man page Source code
DatasetExperiment_factor_boxplot Man page Source code
DatasetExperiment_heatmap Man page Source code
HCA Man page Source code
HSD Man page Source code
HSDEM Man page Source code
MTBLS79_DatasetExperiment Man page Source code
PCA Man page Source code
PLSDA Man page Source code
PLSR Man page Source code
SVM Man page Source code
aov2lme Source code
as_data_frame Man page
as_data_frame,filter_na_count-method Man page
as_data_frame,ttest-method Man page
as_data_frame,wilcox_test-method Man page
ascale Source code
autoscale Man page Source code
balanced_accuracy Man page Source code
blank_filter Man page Source code
blank_filter_hist Man page Source code
bootstrap Man page Source code
calculate Man page
calculate,AUC-method Man page
calculate,balanced_accuracy-method Man page
calculate,r_squared-method Man page
center_colmeans Source code
chart_plot Man page
chart_plot,DatasetExperiment_boxplot,DatasetExperiment-method Man page
chart_plot,DatasetExperiment_dist,DatasetExperiment-method Man page
chart_plot,DatasetExperiment_factor_boxplot,DatasetExperiment-me Man page
chart_plot,DatasetExperiment_heatmap,DatasetExperiment-method Man page
chart_plot,blank_filter_hist,blank_filter-method Man page
chart_plot,compare_dist,DatasetExperiment-method Man page
chart_plot,confounders_lsq_barchart,confounders_clsq-method Man page
chart_plot,confounders_lsq_boxplot,confounders_clsq-method Man page
chart_plot,dfa_scores_plot,DFA-method Man page
chart_plot,feature_boxplot,DatasetExperiment-method Man page
chart_plot,feature_profile,DatasetExperiment-method Man page
chart_plot,fold_change_plot,fold_change-method Man page
chart_plot,fs_line,forward_selection_by_rank-method Man page
chart_plot,glog_opt_plot,glog_transform-method Man page
chart_plot,gs_line,grid_search_1d-method Man page
chart_plot,hca_dendrogram,HCA-method Man page
chart_plot,kfoldxcv_grid,kfold_xval-method Man page
chart_plot,kfoldxcv_metric,kfold_xval-method Man page
chart_plot,kw_p_hist,kw_rank_sum-method Man page
chart_plot,mv_boxplot,DatasetExperiment-method Man page
chart_plot,mv_feature_filter_hist,mv_feature_filter-method Man page
chart_plot,mv_histogram,DatasetExperiment-method Man page
chart_plot,mv_sample_filter_hist,mv_sample_filter-method Man page
chart_plot,pca_biplot,PCA-method Man page
chart_plot,pca_correlation_plot,PCA-method Man page
chart_plot,pca_dstat_plot,PCA-method Man page
chart_plot,pca_loadings_plot,PCA-method Man page
chart_plot,pca_scores_plot,PCA-method Man page
chart_plot,pca_scree_plot,PCA-method Man page
chart_plot,permutation_test_plot,permutation_test-method Man page
chart_plot,plsda_predicted_plot,PLSDA-method Man page
chart_plot,plsda_regcoeff_plot,PLSDA-method Man page
chart_plot,plsda_roc_plot,PLSDA-method Man page
chart_plot,plsda_scores_plot,PLSDA-method Man page
chart_plot,plsda_vip_plot,PLSDA-method Man page
chart_plot,plsr_cook_dist,PLSR-method Man page
chart_plot,plsr_prediction_plot,PLSR-method Man page
chart_plot,plsr_qq_plot,PLSR-method Man page
chart_plot,plsr_residual_hist,PLSR-method Man page
chart_plot,pqn_norm_hist,pqn_norm-method Man page
chart_plot,rsd_filter_hist,rsd_filter-method Man page
chart_plot,svm_plot_2d,SVM-method Man page
chart_plot,tSNE_scatter,tSNE-method Man page
chart_plot,wilcox_p_hist,wilcox_test-method Man page
ci_delta_nu Source code
circleFun Source code
classical_lsq Man page Source code
compare_dist Man page Source code
confounders_clsq Man page Source code
confounders_lsq_barchart Man page Source code
confounders_lsq_boxplot Man page Source code
constant_sum_norm Man page Source code
corr_coef Man page Source code
dfa_scores_plot Man page Source code
dratio_filter Man page Source code
eval_loess Source code
feature_boxplot Man page Source code
feature_profile Man page Source code
filter_by_name Man page Source code
filter_na_count Man page Source code
filter_smeta Man page Source code
first_min Source code
fisher_exact Man page Source code
fold_change Man page Source code
fold_change_int Man page Source code
fold_change_plot Man page Source code
forward_selection_by_rank Man page Source code
fs_line Man page Source code
full_fact Source code
gauss_intersect Source code
get_description Source code
glog_opt_plot Man page Source code
glog_transform Man page Source code
grid_search_1d Man page Source code
gs_line Man page Source code
hca_dendrogram Man page Source code
kfold_xval Man page Source code
kfoldxcv_grid Man page Source code
kfoldxcv_metric Man page Source code
knn_impute Man page Source code
kw_p_hist Man page Source code
kw_rank_sum Man page Source code
linear_model Man page Source code
log_transform Man page Source code
mean_centre Man page Source code
mean_of_medians Man page Source code
mixed_effect Man page Source code
model_apply Man page
model_apply,ANOVA,DatasetExperiment-method Man page
model_apply,HCA,DatasetExperiment-method Man page
model_apply,HSD,DatasetExperiment-method Man page
model_apply,HSDEM,DatasetExperiment-method Man page
model_apply,classical_lsq,DatasetExperiment-method Man page
model_apply,confounders_clsq,DatasetExperiment-method Man page
model_apply,constant_sum_norm,DatasetExperiment-method Man page
model_apply,corr_coef,DatasetExperiment-method Man page
model_apply,filter_smeta,DatasetExperiment-method Man page
model_apply,fisher_exact,DatasetExperiment-method Man page
model_apply,fold_change,DatasetExperiment-method Man page
model_apply,fold_change_int,DatasetExperiment-method Man page
model_apply,knn_impute,DatasetExperiment-method Man page
model_apply,kw_rank_sum,DatasetExperiment-method Man page
model_apply,log_transform,DatasetExperiment-method Man page
model_apply,mean_of_medians,DatasetExperiment-method Man page
model_apply,mixed_effect,DatasetExperiment-method Man page
model_apply,mv_sample_filter,DatasetExperiment-method Man page
model_apply,nroot_transform,DatasetExperiment-method Man page
model_apply,pairs_filter,DatasetExperiment-method Man page
model_apply,pqn_norm,DatasetExperiment-method Man page
model_apply,prop_na,DatasetExperiment-method Man page
model_apply,rsd_filter,DatasetExperiment-method Man page
model_apply,sb_corr,DatasetExperiment-method Man page
model_apply,split_data,DatasetExperiment-method Man page
model_apply,stratified_split,DatasetExperiment-method Man page
model_apply,tSNE,DatasetExperiment-method Man page
model_apply,ttest,DatasetExperiment-method Man page
model_apply,vec_norm,DatasetExperiment-method Man page
model_apply,wilcox_test,DatasetExperiment-method Man page
model_predict Man page
model_predict,DFA,DatasetExperiment-method Man page
model_predict,PCA,DatasetExperiment-method Man page
model_predict,PLSDA,DatasetExperiment-method Man page
model_predict,PLSR,DatasetExperiment-method Man page
model_predict,SVM,DatasetExperiment-method Man page
model_predict,autoscale,DatasetExperiment-method Man page
model_predict,blank_filter,DatasetExperiment-method Man page
model_predict,constant_sum_norm,DatasetExperiment-method Man page
model_predict,dratio_filter,DatasetExperiment-method Man page
model_predict,filter_by_name,DatasetExperiment-method Man page
model_predict,filter_na_count,DatasetExperiment-method Man page
model_predict,filter_smeta,DatasetExperiment-method Man page
model_predict,glog_transform,DatasetExperiment-method Man page
model_predict,linear_model,DatasetExperiment-method Man page
model_predict,mean_centre,DatasetExperiment-method Man page
model_predict,mv_feature_filter,DatasetExperiment-method Man page
model_predict,mv_sample_filter,DatasetExperiment-method Man page
model_predict,pareto_scale,DatasetExperiment-method Man page
model_predict,vec_norm,DatasetExperiment-method Man page
model_reverse Man page
model_reverse,autoscale,DatasetExperiment-method Man page
model_reverse,mean_centre,DatasetExperiment-method Man page
model_train Man page
model_train,DFA,DatasetExperiment-method Man page
model_train,PCA,DatasetExperiment-method Man page
model_train,PLSDA,DatasetExperiment-method Man page
model_train,PLSR,DatasetExperiment-method Man page
model_train,SVM,DatasetExperiment-method Man page
model_train,autoscale,DatasetExperiment-method Man page
model_train,blank_filter,DatasetExperiment-method Man page
model_train,constant_sum_norm,DatasetExperiment-method Man page
model_train,dratio_filter,DatasetExperiment-method Man page
model_train,filter_by_name,DatasetExperiment-method Man page
model_train,filter_na_count,DatasetExperiment-method Man page
model_train,filter_smeta,DatasetExperiment-method Man page
model_train,glog_transform,DatasetExperiment-method Man page
model_train,linear_model,DatasetExperiment-method Man page
model_train,mean_centre,DatasetExperiment-method Man page
model_train,mv_feature_filter,DatasetExperiment-method Man page
model_train,mv_sample_filter,DatasetExperiment-method Man page
model_train,pareto_scale,DatasetExperiment-method Man page
model_train,vec_norm,DatasetExperiment-method Man page
mv_boxplot Man page Source code
mv_feature_filter Man page Source code
mv_feature_filter_hist Man page Source code
mv_histogram Man page Source code
mv_sample_filter Man page Source code
mv_sample_filter_hist Man page Source code
nroot_transform Man page Source code
pairs_filter Man page Source code
pareto_scale Source code
pca_biplot Man page Source code
pca_correlation_plot Man page Source code
pca_dstat_plot Man page Source code
pca_loadings_plot Man page Source code
pca_scores_plot Man page Source code
pca_scree_plot Man page Source code
permutation_test Man page Source code
permutation_test_plot Man page Source code
permute_sample_order Man page Source code
plsda_predicted_plot Man page Source code
plsda_regcoeff_plot Man page Source code
plsda_roc_plot Man page Source code
plsda_scores_plot Man page Source code
plsda_vip_plot Man page Source code
plsr_cook_dist Man page Source code
plsr_prediction_plot Man page Source code
plsr_qq_plot Man page Source code
plsr_residual_hist Man page Source code
pqn_norm Man page Source code
pqn_norm_hist Man page Source code
prob Source code
prop_na Man page Source code
pscale Source code
r_squared Man page Source code
rsd_filter Man page Source code
rsd_filter_hist Man page Source code
run Man page
run,bootstrap,DatasetExperiment,metric-method Man page
run,forward_selection_by_rank,DatasetExperiment,metric-method Man page
run,grid_search_1d,DatasetExperiment,metric-method Man page
run,kfold_xval,DatasetExperiment,metric-method Man page
run,permutation_test,DatasetExperiment,metric-method Man page
run,permute_sample_order,DatasetExperiment,metric-method Man page
sb_corr Man page Source code
scale_colour_Publication Source code
scale_fill_Publication Source code
set_scale Source code
split_data Man page Source code
stratified_split Man page Source code
structToolbox Man page
svm_plot_2d Man page Source code
tSNE Man page Source code
tSNE_scatter Man page Source code
theme_Publication Source code
ttest Man page Source code
unascale Source code
uncenter_colmeans Source code
var_nu Source code
vec_norm Man page Source code
vips Source code Source code
wilcox_p_hist Man page Source code
wilcox_test Man page Source code
computational-metabolomics/structToolbox documentation built on Nov. 17, 2020, 2:27 p.m.