sipss/AlpsNMR
Automated spectraL Processing System for NMR

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368
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58
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sipss/AlpsNMR: Automated spectraL Processing System for NMR
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API

API for sipss/AlpsNMR
Automated spectraL Processing System for NMR

Global functions
%>% Man page
.DollarNames Man page
.DollarNames.nmr_dataset_family Source code
.refresh_nmr_dataset_rds Source code
AlpsNMR Man page
AlpsNMR-package Man page
HMDB_blood Man page
HMDB_cell Man page
HMDB_urine Man page
Parameters_blood Man page
Parameters_cell Man page
Parameters_urine Man page
Peak_detection Man page
Pipe_normalization Man page
Pipelines Man page
ROI_blood Man page
ROI_cell Man page
ROI_urine Man page
SummarizedExperiment_to_nmr_data_1r Man page Source code
SummarizedExperiment_to_nmr_dataset_peak_table Man page Source code
[.nmr_dataset Man page
[.nmr_dataset_1D Man page
[.nmr_dataset_peak_table Man page
`[.nmr_dataset_1D` Source code
`[.nmr_dataset_peak_table` Source code
`[.nmr_dataset` Source code
`names<-.nmr_dataset_family` Source code
abort_if_not Source code
are_ppm_regions_excluded Source code
as.data.frame.nmr_dataset_peak_table Man page Source code
batman_get_full_filename Source code
bp_VIP_analysis Man page Source code
bp_kfold_VIP_analysis Man page Source code
bruker_merge_meta_pdata Source code
callDetectSpecPeaks Source code
callback_outer_cv_auroc_vip Source code
callback_plsda_auroc_vip Source code
choose_best_nlv Source code
choose_best_nlv_diagnostic_info Source code
choose_best_nlv_impl Source code
computes_peak_width_ppm Source code
convert_field Source code
create_df_from_jdx_sample Source code
create_sample_names Source code
curl_download_retry Source code
decimate_axis Source code
do_cv Source code
download_MTBLS242 Man page Source code
estimate_num_clusters Source code
file_lister Man page Source code
files_to_rDolphin Man page Source code
filter Man page
filter.nmr_dataset_family Man page Source code
format.nmr_dataset Man page Source code
format.nmr_dataset_1D Man page Source code
format.nmr_dataset_peak_table Man page Source code
fun_choose_best_ncomp_auc_threshold Source code
get_geom_text Source code
get_integration_with_metadata Man page
get_max_dist_ppb_for_num_clusters Source code
get_norm_rmse Source code
get_peak_bounds Source code
get_test_accuracy Source code
get_vars_from_aes Source code
get_vars_from_aes_string Source code
guess_shape_and_submatrix_shape Source code
hmdb Man page
infer_dim_pulse_nuclei Source code
interpolate_1d Source code
is.nmr_dataset Man page Source code
is.nmr_dataset_1D Man page Source code
is.nmr_dataset_peak_table Man page Source code
is_ppm_included Source code
is_using_aes_string Source code
list_of_lists_to_tibble Source code
load_and_save_functions Man page
lorentzian Source code
mahalanobis_distance Source code
models_stability_plot_bootstrap Man page Source code
models_stability_plot_plsda Man page Source code
names.nmr_dataset_family Source code
new_nmr_data_analysis_method Man page Source code
new_nmr_dataset Man page Source code
new_nmr_dataset_1D Man page Source code
new_nmr_dataset_peak_table Man page Source code
nmr_align Man page Source code
nmr_align_find_ref Man page Source code
nmr_autophase Man page Source code
nmr_baseline_estimation Man page Source code
nmr_baseline_removal Man page Source code
nmr_baseline_threshold Man page Source code
nmr_baseline_threshold_plot Man page Source code
nmr_baseline_threshold_plot_aes_string Source code
nmr_batman Man page
nmr_batman_export_dataset Man page Source code
nmr_batman_metabolites_list Man page Source code
nmr_batman_multi_data_user Man page Source code
nmr_batman_multi_data_user_hmdb Man page Source code
nmr_batman_options Man page Source code
nmr_batman_write_options Man page Source code
nmr_build_peak_table Man page Source code
nmr_data Man page Source code
nmr_data.nmr_dataset_1D Man page Source code
nmr_data.nmr_dataset_peak_table Source code
nmr_data<- Man page
nmr_data<-.nmr_dataset_1D Man page
nmr_data_1r_to_SummarizedExperiment Man page Source code
nmr_data_analysis Man page Source code
nmr_data_analysis_method Man page
nmr_dataset Man page
nmr_dataset_1D Man page
nmr_dataset_family Man page
nmr_dataset_load Man page Source code
nmr_dataset_peak_table Man page
nmr_dataset_peak_table_to_SummarizedExperiment Man page Source code
nmr_dataset_save Man page Source code
nmr_detect_peaks Man page Source code
nmr_detect_peaks_plot Man page Source code
nmr_detect_peaks_plot_overview Man page Source code
nmr_detect_peaks_plot_peaks Man page Source code
nmr_detect_peaks_tune_snr Man page Source code
nmr_exclude_region Man page Source code
nmr_exclude_region.nmr_dataset_1D Man page Source code
nmr_export_data_1r Man page Source code
nmr_get_excluded_regions Source code
nmr_get_peak_distances Man page Source code
nmr_identify_regions_blood Man page Source code
nmr_identify_regions_cell Man page Source code
nmr_identify_regions_urine Man page Source code
nmr_integrate_peak_positions Man page
nmr_integrate_regions Man page Source code
nmr_integrate_regions.nmr_dataset_1D Man page Source code
nmr_interpolate_1D Man page Source code
nmr_interpolate_1D.nmr_dataset Man page Source code
nmr_meta_add Man page Source code
nmr_meta_add_tidy_excel Man page Source code
nmr_meta_export Man page
nmr_meta_get Man page Source code
nmr_meta_get_column Man page Source code
nmr_meta_groups Man page Source code
nmr_normalize Man page Source code
nmr_normalize_add_extra_info Source code
nmr_normalize_extra_info Man page Source code
nmr_pca_build_model Man page Source code
nmr_pca_build_model.nmr_dataset_1D Man page Source code
nmr_pca_loadingplot Man page Source code
nmr_pca_outliers Man page Source code
nmr_pca_outliers_filter Man page Source code
nmr_pca_outliers_plot Man page Source code
nmr_pca_outliers_robust Man page Source code
nmr_pca_plot_variance Man page Source code
nmr_pca_plots Man page
nmr_pca_scoreplot Man page Source code
nmr_peak_clustering Man page Source code
nmr_peak_clustering_plot Man page Source code
nmr_ppm_resolution Man page Source code
nmr_ppm_resolution.nmr_dataset Man page Source code
nmr_ppm_resolution.nmr_dataset_1D Man page Source code
nmr_read_bruker_fid Man page Source code
nmr_read_sample_bruker Source code
nmr_read_samples Man page Source code
nmr_read_samples_bruker Source code
nmr_read_samples_dir Man page Source code
nmr_read_samples_jdx Source code
nmr_zip_bruker_samples Man page Source code
norm_pqn Source code
parse_title_file Source code
peak2peak_distance Source code
peakList_to_dataframe Source code
peak_data_to_peakList Source code
peaklist_accept_peaks Man page Source code
peaklist_fit_lorentzians Man page Source code
permutation_test_model Man page Source code
permutation_test_plot Man page Source code
pipe_add_metadata Man page Source code
pipe_exclude_regions Man page Source code
pipe_filter_samples Man page Source code
pipe_interpolate_1D Man page Source code
pipe_load_samples Man page Source code
pipe_normalization Man page Source code
pipe_outlier_detection Man page Source code
pipe_pakdet_align Man page
pipe_peak_integration Man page Source code
pipe_peakdet_align Man page Source code
plot.nmr_dataset_1D Man page Source code
plot_bootstrap_multimodel Man page Source code
plot_interactive Man page Source code
plot_plsda_multimodel Man page Source code
plot_plsda_samples Man page Source code
plot_vip_scores Man page Source code
plot_webgl Man page Source code
plot_with_aes Source code
plot_with_aes_string Source code
plsda_auroc Source code
plsda_auroc_vip_compare Man page Source code
plsda_auroc_vip_method Man page Source code
plsda_build Source code
plsda_vip Source code
ppm_resolution Man page Source code
prepare_aes Source code
print.nmr_dataset Man page Source code
print.nmr_dataset_1D Man page Source code
print.nmr_dataset_peak_table Man page Source code
process_block Source code
progress_bar_end Source code
progress_bar_new Source code
progress_bar_update Source code
random_subsampling Man page Source code
read_acqus_file Source code
read_bin_data Source code
read_bruker_metadata Source code
read_bruker_param Source code
read_bruker_pdata Man page Source code
read_bruker_sample Source code
read_jdx Source code
read_levels Source code
read_orig_file Source code
read_pdata_title_file Source code
read_procs_file Source code
reexports Man page
refine_lorentzian_fit_with_nls Source code
regions_from_peak_table Source code
rename Man page
rename.nmr_dataset_family Source code
require_pkgs Source code
rough_baseline Source code
save_files_to_rDolphin Man page Source code
save_profiling_output Man page Source code
set_peak_distances_within_groups Source code
show_progress_bar Source code
signif_transformer Source code
split_build_perform Source code
split_double_cv Source code
strip_comments Source code
tibble_lists_columns_to_vector_columns Source code
tidy Man page
tidy.nmr_dataset_1D Man page Source code
tidy_spectra_baseline_and_threshold Source code
to_ASICS Man page Source code
to_ChemoSpec Man page Source code
train_models_with_only_vip_features Source code
validate_nmr_dataset Man page Source code
validate_nmr_dataset_1D Man page Source code
validate_nmr_dataset_family Man page Source code
validate_nmr_dataset_peak_table Man page Source code
verify_axisn Source code
verify_dimensionality Source code
zzz Man page
sipss/AlpsNMR documentation built on Aug. 13, 2024, 5:11 p.m.

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