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mkdocs.yml
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site_name: mzmine documentation
site_url: https://mzmine.github.io/mzmine_documentation/
edit_uri: https://github.com/mzmine/mzmine_documentation/edit/master/docs/
repo_name: mzmine/mzmine_documentation
repo_url: https://github.com/mzmine/mzmine_documentation
use_directory_urls: false
nav:
- Home page: index.md
- Getting started: getting_started.md
- User account: services/users.md
- Learners corner: learners_corner.md
- Main window overview: main-window-overview.md
- Processing wizard: wizard.md
- Data conversion: data_conversion.md
- Performance options: performance.md
- Command line tool (batch mode): commandline_tool.md
- Integration to other tools: tool_integration.md
# - Citations: citations.md
- Processing modules:
- I/O:
- Raw data import: module_docs/io/data-import.md
- Raw data export: module_docs/io/data-export.md
- Feature list import: module_docs/io/feat-list-import.md
- Feature list export: module_docs/io/feat-list-export.md
- Export to other software: module_docs/io/data-exchange-with-other-software.md
- Spectral library export: module_docs/io_spectral_library_export/spectral_library_generation.md
# TODO Add feature list import/export
- File merging:
- Raw data files merging: module_docs/featdet_file_merging/raw-files-merging.md
- Mobility scan merging: module_docs/featdet_mobility_scan_merging/mobility-scan-merging.md
- Raw data filtering:
- Scan by scan filtering: module_docs/filter_raw_data/filter-scan-by-scan.md
- Crop filter: module_docs/filter_raw_data/crop-filter.md
- Baseline corrections: module_docs/filter_raw_data/baseline-corrections.md
- Align scans: module_docs/filter_raw_data/align-scans.md
- Scan smoothing: module_docs/filter_raw_data/scan_smoothing.md
- Mass detection:
- Mass detection: module_docs/featdet_mass_detection/mass-detection.md
- Mass detection algorithms: module_docs/featdet_mass_detection/mass-detection-algorithms.md
- FTMS shoulder peak finder: module_docs/featdet_mass_detection/FTMS-shoulder-peak-filter.md
- Mass calibration: module_docs/featdet_mass_detection/mass-calibration.md
- LC-MS feature detection:
- ADAP Chromatogram builder: module_docs/lc-ms_featdet/featdet_adap_chromatogram_builder/adap-chromatogram-builder.md
- GridMass: module_docs/lc-ms_featdet/featdet_gridmass/gridmass.md
- Targeted feature detection: module_docs/lc-ms_featdet/targeted_featdet/targeted-featdet.md
- Feature detection results: module_docs/lc-ms_featdet/featdet_results/featdet_results.md
- LC-IMS-MS feature detection:
# TODO Rework this one
- Ion mobility expander: module_docs/lc-ims-ms_featdet/featdet_ims_expander/ims-expander.md
- Ion mobility trace builder: module_docs/lc-ims-ms_featdet/featdet_ion_mobility_trace_builder/ion-mobility-trace-builder.md
- Recursive IMS builder: module_docs/lc-ims-ms_featdet/recursive_ims_builder/recursive-ims-builder.md
- MS imaging feature detection:
- Image builder: module_docs/imaging_featdet/featdet_image_builder/image-builder.md
- Smoothing: module_docs/featdet_smoothing/smoothing.md
- Resolving:
- Local minimum resolver: module_docs/featdet_resolver_local_minimum/local-minimum-resolver.md
- ADAP resolver: module_docs/featdet_resolver_adap/adap-resolver.md
- Baseline resolver: module_docs/featdet_resolver_baseline/baseline-resolver.md
- CentWave resolver: module_docs/featdet_resolver_centwave/centwave-resolver.md
- Noise amplitude resolver: module_docs/featdet_resolver_noise_ampl/noise-ampl-resolver.md
- Savitzky-Golay resolver: module_docs/featdet_resolver_savitzky-golay/savitzky-golay-resolver.md
# TODO Add mobilogram binning
- Spectral deconvolution (GC):
- GC-EI spectral deconvolution: module_docs/featdet_spectraldeconvolutiongc/spectraldeconvolutiongc.md
#- Hierarchical clustering: module_docs/featdet_hierarch_clustering/featdet_hierarch_clustering.md
#- Multivariate curve resolution: module_docs/featdet_multivariate_curve_res/featdet_multivar_curve_res.md
- CCS calibration: module_docs/id_ccs_calibration/ccs_calibration.md
- MS2 scan pairing: module_docs/featdet_ms2_scan_pairing/ms2_scan_pairing.md
- MALDI MS2 scan pairing (SIMSEF): module_docs/featdet_ms2_scan_pairing/ms2_maldi_scan_pairing.md
- Isotope filtering:
- 13C isotope filter (isotope grouper): module_docs/filter_isotope_filter/isotope_filter.md
- Isotope pattern finder: module_docs/filter_isotope_finder/isotope_finder.md
- Isotope peak scanner: module_docs/filter_isotope_peak_scanner/isotope_peak_scanner.md
- Feature grouping:
- Correlation grouping: module_docs/id_ion_networking/metacorr/metacorr.md
- Ion Identity Networking: module_docs/id_ion_networking/iin/iin.md
- Spectral / Molecular Networking: module_docs/group_spectral_net/molecular_networking.md
- Feature list filtering:
- Duplicate feature filter: module_docs/filter_duplicate_features/duplicate_feature_filter.md
- Feature list rows filter: module_docs/feature_list_row_filter/feature_list_rows_filter.md
- Feature filter: module_docs/feature_filter/feature_filter.md
- Peak comparison rows filter: module_docs/filter_peakcomparison_row_filter/filter_peakcomparison_row_filter.md
- Neutral loss filter: module_docs/filter_neutral_loss/filter_neutral_loss.md
- m/z mobility region extraction: module_docs/filter_mobilitymzregionextraction/filter_mobilitymzregionextraction.md
- Feature list blank subtraction: module_docs/filter_blanksubtraction/filter_blanksubtraction.md
- Alignment:
- Join aligner: module_docs/align_join_aligner/join_aligner.md
- Merge lists: module_docs/align_merge_lists/align_merge_lists.md
- RANSAC aligner: module_docs/align_ransac/align_ransac.md
# - Hierachical aligner (GC): module_docs/align_hierarch/align_hierarch.md
# - ADAP aligner (GC): module_docs/align_adap/align_adap_gc.md
- GC-EI aligner: module_docs/align_gcei/align_gc_ei.md
- LC Image Aligner: module_docs/align_lc-image/align_lc-image.md
- Gap filling:
- Peak finder: module_docs/gapfill_peak_finder/gap-filling.md
- Same RT and m/z range gap filler: module_docs/gapfill_same_mz_and_RT_range/same_mz_and_RT_range_gap_filler.md
- Normalization:
- Retention time calibration: module_docs/norm_rt_calibration/norm_rt_calibration.md
- Linear normalizer: module_docs/norm_linear/norm_linear.md
- Standard compound normalizer: module_docs/norm_stand_cmpd/norm_stand_cmpd.md
# TODO decide what to do with spectral lib creation
# - Spectral library creation: module_docs/id_spectral_library_creation/spectral_library_creation.md
- Precursor mass search:
- Local database search: module_docs/id_prec_local_cmpd_db/local-cmpd-db-search.md
- Precursor search in local spectral MS/MS library: module_docs/id_prec_local_spectra_lib/local-spectra-lib-search.md
# - Online compound database search: module_docs/id_prec_online_db/online-cmpd-db-search.md
- Spectra search:
- Spectral library search: module_docs/id_spectral_library_search/spectral_library_search.md
- NIST MS search: module_docs/id_spectra_NIST/NIST-ms-search.md
- Chemical formula prediction: module_docs/id_spectra_chem_formula/chem-formula-pred.md
- Lipid annotation: module_docs/id_lipid_annotation/lipid-annotation.md
- MS2 similarity search: module_docs/id_ms2_similarity/ms2-similarity-search.md
- Other parameters:
- Merge MS/MS: module_docs/io/merge_ms2_kai.md
- Spectra similarity: module_docs/align_join_aligner/spectra_similarity.md
- Visualization modules:
- Visualization overview: visualization_modules/visualization_overview/visualization-overview.md
- MS data visualisation:
- Raw data overview: visualization_modules/raw_data_overview/raw_data_overview.md
- Additional tools: visualization_modules/raw_data_overview/raw_data_additional.md
- Ion mobility data visualisation: visualization_modules/ims_raw_data_overview/IM-data-visualisation.md
- Image viewer: visualization_modules/image_raw_data/image_viewer.md
- Image co-localization: module_docs/group_imagecorrelate/image-colocalization.md
- Processed data visualition:
- MSMS Visualizer: visualization_modules/msmsplot/msms-plot.md
- Interactive Ion Identity Molecular Networks: visualization_modules/interactive_ion_id_netw/interactive_ion_id_netw.md
- Feature histograms: visualization_modules/feature_histograms/feature_hist.md
- 4D features plot (Kendrick): visualization_modules/kendrickmass/kendrick_mass_plot.md
- Van Krevelen plot: visualization_modules/vankrevelen/van_krevelen_plot.md
- ECN (Equivalent Carbon Number) models: visualization_modules/ecn_plots/ecn_plots.md
- Lipid annotation summary: visualization_modules/lipid_annotation_summary/lipid_annotation_summary.md
- Additional tools: visualization_modules/processed_additional/processed_additional.md
- Massvoltammogram: visualization_modules/massvoltammogram/massvoltammogram.md
- Workflows:
- Untargeted LC-MS workflow: workflows/lcmsworkflow/lcms-workflow.md
- Untargeted LC-IMS-MS workflow: workflows/imsworkflow/ion-mobility-data-processing-workflow.md
- Untargeted GC-MS workflow: workflows/gcmsworkflow/gcms-workflow.md
- Untargeted MS imaging workflow: workflows/imagingworkflow/imaging-workflow.md
- Batch processing: workflows/batch_processing/batch-processing.md
- Library generation: workflows/librarygeneration/library_generation.md
- SIMSEF: workflows/simsef/simsef_workflow.md
- Tools:
- SIMSEF scheduler: module_docs/tools_simsef/simsef.md
- Additional resources:
- General Terminology: terminology/general-terminology.md
- IMS Terminology: terminology/ion-mobility-terminology.md
- LC-MS and LC-IMS-MS data comparison: workflows/imsworkflow/lc-ms-and-lc-ims-ms-data-comparison.md
# - Kendrick mass defect: module_docs/feature_list_row_filter/kendrick_mass_defect.md
- Spectral similarity measures: module_docs/id_spectral_library_search/spectral-similarity-measures.md
- Contribute:
- Coding:
- mzmine development (in IntelliJ): contribute_intellij.md
- Upgrade JDK version: coding/upgrade_jdk_version.md
- General structure: coding/general_structure.md
# - macOS code signing: coding/macos_signing.md
- Module development: coding/module_development.md
- Modules list: coding/module_list.md
# TODO Finish writing these
# - Raw data structure: coding/raw_data_structure.md
# - Feature data structure: coding/feature_data_structure.md
# - Example module - Spectral entropy: coding/example_module.md
- Contribute to documentation: contribute.md
- Documentation template: contribute_docu_template.md
- Acknowledgements: wikiacknowledgements.md
- Troubleshooting: troubleshooting.md
- Changelog: changelog.md
- Workshops: workshops.md
copyright: This documentation is licensed under the MIT License (MIT).
extra_css:
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theme:
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logo: img/mzmine_logo_white.png
palette:
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primary: custom
plugins:
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- git-authors:
show_contribution: false
- git-revision-date-localized:
type: datetime
- with-pdf:
output_path: documentation.pdf
author: The mzmine Community
cover_title: mzmine
cover_subtitle: Documentation
cover_logo: docs/img/MZmine_logo_CMYK.png
markdown_extensions:
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permalink: true
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# https://squidfunk.github.io/mkdocs-material/reference/formatting/
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