forked from mzmine/mzmine_documentation
-
Notifications
You must be signed in to change notification settings - Fork 0
/
mkdocs.yml
202 lines (189 loc) · 10.9 KB
/
mkdocs.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
site_name: MZmine 3 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
- Main window overview: main-window-overview.md
- Processing wizard: wizard.md
- Data conversion: data_conversion.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
# 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
- 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):
- 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
- 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
# TODO Add feature grouping
- 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
- 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
- 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
- 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
- Batch processing: workflows/batch_processing/batch-processing.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
- Performance options: performance.md
- Command line tool (batch mode): commandline_tool.md
- Contribute:
- Coding:
- General structure: coding/general_structure.md
- macOS code signing: coding/macos_signing.md
- MZmine development (in IntelliJ): contribute_intellij.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
- Changelog: changelog.md
- Workshops: workshops.md
copyright: This documentation is licensed under the MIT License (MIT).
extra_css:
- css/extra.css
theme:
name: material
logo: img/MZMine_logo_white.png
plugins:
- search
- git-authors:
show_contribution: false
- git-revision-date-localized:
type: datetime
- with-pdf:
output_path: documentation.pdf
author: The MZmine Community
cover_title: MZmine 3
cover_subtitle: Documentation
cover_logo: docs/img/MZmine_logo_CMYK.png
markdown_extensions:
- toc:
permalink: true
- admonition
- attr_list
# https://squidfunk.github.io/mkdocs-material/reference/formatting/
# superscript ^13^C subscript H~2~O
# key combinations: ++ctrl+alt+del++
- pymdownx.caret
- pymdownx.keys
- pymdownx.mark
- pymdownx.tilde
- pymdownx.superfences:
# make exceptions to highlighting of code:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:mermaid2.fence_mermaid
- pymdownx.details
- pymdownx.emoji:
emoji_index: !!python/name:materialx.emoji.twemoji
emoji_generator: !!python/name:materialx.emoji.to_svg
- pymdownx.arithmatex:
generic: true
extra_javascript:
- javascripts/mathjax.js
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js