Files in sipss/AlpsLCMS
Signal processing of LC-MS metabolomics
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AlpsLCMS.Rproj
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/HMDB_metabolites.R
R/clustering.R
R/data_analysis.R
R/diagnose.R
R/known_metabolites.R
R/metabolite_identification.R
R/parameter_optimization.R
R/plsda.R
R/post_processing.R
R/pre_processing.R
R/raw_converter.R
R/sample_management.R
R/utils.R
R/utils_future.R
README.md
_pkgdown.yml
data/HMDB_db.csv
data/HMDB_db.rda
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/NIHSlcms_MTBLS665.html
docs/articles/index.html
docs/articles/introduction-to-alpslcms.html
docs/articles/introduction-to-alpslcms_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/introduction-to-alpslcms_files/figure-html/Alignment-1.png
docs/articles/introduction-to-alpslcms_files/figure-html/Params Data reduction-1.png
docs/articles/introduction-to-alpslcms_files/figure-html/Peak detection-1.png
docs/articles/introduction-to-alpslcms_files/figure-html/unnamed-chunk-12-1.png
docs/articles/introduction-to-alpslcms_files/figure-html/unnamed-chunk-12-2.png
docs/articles/introduction-to-alpslcms_files/figure-html/unnamed-chunk-5-1.png
docs/articles/introduction-to-alpslcms_files/figure-html/unnamed-chunk-5-2.png
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docs/articles/introduction-to-alpslcms_files/figure-html/unnamed-chunk-8-2.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/HMDB_db.html
docs/reference/IPO_group_peaks.html
docs/reference/PeakDensityPar.html
docs/reference/PeakGroupsPar-1.png
docs/reference/PeakGroupsPar-2.png
docs/reference/PeakGroupsPar.html
docs/reference/adjustRT.html
docs/reference/assignation_neg_HMDB.html
docs/reference/assignation_pos_HMDB.html
docs/reference/clustering.html
docs/reference/cromplot.html
docs/reference/default_peakpicking_params.html
docs/reference/do.findmain.html
docs/reference/do_findmain.html
docs/reference/feature_reduction.html
docs/reference/feature_values.html
docs/reference/featurevalues.html
docs/reference/figures/AlpsLCMSlogo.png
docs/reference/filterMassAcquisition.html
docs/reference/find_peaks_cwp.html
docs/reference/getRamSt.html
docs/reference/groupPeaks.html
docs/reference/index.html
docs/reference/install_RawConverter.html
docs/reference/is.negative.html
docs/reference/is.positive.html
docs/reference/known_metabolites.html
docs/reference/labelled_adducts.html
docs/reference/labelling.html
docs/reference/lcms_convert_ipo_to_xcms.html
docs/reference/lcms_dataset_load.html
docs/reference/lcms_dataset_save.html
docs/reference/lcms_default_peakpicking_params.html
docs/reference/lcms_default_retcorgroup_params.html
docs/reference/lcms_diagnose.html
docs/reference/lcms_fill_chrom_peaks.html
docs/reference/lcms_filter_mz.html
docs/reference/lcms_filter_polarity.html
docs/reference/lcms_filter_rt_min.html
docs/reference/lcms_filter_sample_type.html
docs/reference/lcms_identify_metabolites.html
docs/reference/lcms_list_mzxml_samples.html
docs/reference/lcms_meta_add.html
docs/reference/lcms_meta_export.html
docs/reference/lcms_meta_read.html
docs/reference/lcms_peak_annotation.html
docs/reference/lcms_peak_table_boxplots.html
docs/reference/lcms_peak_table_pca.html
docs/reference/lcms_peakpicking_optimization.html
docs/reference/lcms_plot_chrom.html
docs/reference/lcms_plot_chrom_peak_image.html
docs/reference/lcms_plot_metabolites.html
docs/reference/lcms_plot_tics.html
docs/reference/lcms_raw_data.html
docs/reference/lcms_raw_to_mzxml.html
docs/reference/lcms_read_ipo_to_xcms.html
docs/reference/lcms_read_samples.html
docs/reference/lcms_rearrange_datafiles_by_class.html
docs/reference/lcms_retcorgroup_optimization.html
docs/reference/lcms_retention_time_alignment_plot.html
docs/reference/lcms_sig_peaks_table.html
docs/reference/lcms_spectral_sig_features.html
docs/reference/lcms_tics.html
docs/reference/lcms_to_mait.html
docs/reference/lcms_write_opt_params.html
docs/reference/lcms_write_parameter_table.html
docs/reference/obiAdjust_Rtime.html
docs/reference/peakpicking_optimization.html
docs/reference/phData.html
docs/reference/reexports.html
inst/extdata/dataset_pos.rds
inst/extdata/default_peakpicking_params.rds
inst/extdata/default_retcorgroup_params.rds
inst/extdata/exported_metadata.xlsx
inst/extdata/metadata.xlsx
inst/extdata/params.csv
inst/extdata/params.rds
inst/extdata/preproc_params.rds
inst/extdata/result_retcorgroup.rds
inst/extdata/sig_table.rds
man/HMDB_db.Rd
man/IPO_group_peaks.Rd
man/PeakDensityPar.Rd
man/PeakGroupsPar.Rd
man/adjustRT.Rd
man/assignation_neg_HMDB.Rd
man/assignation_pos_HMDB.Rd
man/bp_VIP_analysis.Rd
man/bp_kfold_VIP_analysis.Rd
man/check_dataset.Rd
man/clustering.Rd
man/cromplot.Rd
man/default_peakpicking_params.Rd
man/do_findmain.Rd
man/feature_reduction.Rd
man/feature_values.Rd
man/figures/AlpsLCMSlogo.png
man/filterMassAcquisition.Rd
man/find_peaks_cwp.Rd
man/getRamSt.Rd
man/groupPeaks.Rd
man/install_RawConverter.Rd
man/is.negative.Rd
man/is.positive.Rd
man/known_metabolites.Rd
man/lcms_convert_ipo_to_xcms.Rd
man/lcms_data_analysis.Rd
man/lcms_data_analysis_method.Rd
man/lcms_dataset_load.Rd
man/lcms_dataset_save.Rd
man/lcms_default_retcorgroup_params.Rd
man/lcms_diagnose.Rd
man/lcms_fill_chrom_peaks.Rd
man/lcms_filter_mz.Rd
man/lcms_filter_polarity.Rd
man/lcms_filter_rt_min.Rd
man/lcms_filter_sample_type.Rd
man/lcms_identify_metabolites.Rd
man/lcms_list_mzxml_samples.Rd
man/lcms_meta_add.Rd
man/lcms_meta_export.Rd
man/lcms_meta_read.Rd
man/lcms_peak_annotation.Rd
man/lcms_peak_table_boxplots.Rd
man/lcms_peak_table_pca.Rd
man/lcms_plot_chrom.Rd
man/lcms_plot_chrom_peak_image.Rd
man/lcms_plot_metabolites.Rd
man/lcms_plot_tics.Rd
man/lcms_raw_data.Rd
man/lcms_raw_to_mzxml.Rd
man/lcms_read_ipo_to_xcms.Rd
man/lcms_read_samples.Rd
man/lcms_rearrange_datafiles_by_class.Rd
man/lcms_retcorgroup_optimization.Rd
man/lcms_retention_time_alignment_plot.Rd
man/lcms_sig_peaks_table.Rd
man/lcms_spectral_sig_features.Rd
man/lcms_tics.Rd
man/lcms_to_mait.Rd
man/lcms_write_opt_params.Rd
man/lcms_write_parameter_table.Rd
man/models_stability_plot_bootstrap.Rd
man/models_stability_plot_plsda.Rd
man/obiAdjust_Rtime.Rd
man/peakpicking_optimization.Rd
man/permutation_test_model.Rd
man/permutation_test_plot.Rd
man/phData.Rd
man/plot_bootstrap_multimodel.Rd
man/plot_plsda_multimodel.Rd
man/plot_plsda_samples.Rd
man/plot_vip_scores.Rd
man/plsda_auroc_vip_compare.Rd
man/plsda_auroc_vip_method.Rd
man/random_subsampling.Rd
man/reexports.Rd
tests/testthat.R
tests/testthat/test_identification.R
tests/testthat/test_loading.R
tests/testthat/test_prueba.R
tests/testthat/test_tics.R
vignettes/IPO/rsm_1.jpg
vignettes/introduction-to-alpslcms.R
vignettes/introduction-to-alpslcms.Rmd
vignettes/introduction-to-alpslcms.html
vignettes/spectra/fill.mspLib
vignettes/spectra/findmainPlots.pdf
