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mkdocs.yml
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site_name: GNPS Documentation
site_url: https://ccms-ucsd.github.io/GNPSDocumentation/
edit_uri: https://github.com/CCMS-UCSD/GNPSDocumentation/edit/master/docs/
repo_name: CCMS-UCSD/GNPSDocumentation
repo_url: https://github.com/CCMS-UCSD/GNPSDocumentation
nav:
- GNPS Introduction: index.md
- Is my data compatible with GNPS?: isgnpsright.md
- Frequently Asked Questions: faq.md
- Superquick Start Guide: superquickstart.md
- Quick Start Guide: quickstart.md
- GNPS Analysis Tools Overview: gnpsanalysisoverview.md
- GNPS Lexicon: lexicon.md
- Mass Spec/Computational Background:
# - Targeted vs Untargeted: massspecbackground/targeteduntargeted.md
# - Tandem Mass Spectrometry (MS/MS): massspecbackground/tandemms.md
# - Methods of Identification: massspecbackground/identification.md
# - Method of Quantification: massspecbackground/quantification.md
- Molecular Networking: massspecbackground/networkingtheory.md
- Data Preparation/Upload:
- Mass Spectrometry File Conversion: fileconversion.md
- File Conversion (Waters): fileconversion_waters.md
- Shimazdu Gotchas: shimadzu.md
- GNPS File Upload: fileupload.md
- Metadata: metadata.md
- Recommended Data Analysis:
- Molecular Networking: networking.md
- GC-MS Molecular Networking:
- GC-MS on GNPS: gcanalysis.md
- GC-MS Deconvolution: gc-ms-deconvolution.md
- GC-MS Library Search and Molecular Networking: gc-ms-library-molecular-network.md
- Molecular Networking Views: networkingviews.md
- Spectral Library Search: librarysearch.md
- MASST Search (Mass Search Tool): masst.md
- Result Views Navigation: resultviews.md
- Mass Spec Data Visualization:
- GNPS Dashboard: lcms-dashboard.md
- GNPS Dataset Explorer: gnpsdatasetexplorer.md
- Metabolomics Spectrum Resolver: usi.md
- GNPS Dashboard Use Cases: dashboard_use_cases.md
- Advanced Data Analysis:
- Molecular Networking Files: networkingfiles.md
- Feature Based Molecular Networking:
- FBMN Workflow: featurebasedmolecularnetworking.md
- FBMN with MZmine : featurebasedmolecularnetworking-with-mzmine2.md
- FBMN with MS-DIAL: featurebasedmolecularnetworking-with-ms-dial.md
- FBMN with XCMS: featurebasedmolecularnetworking-with-xcms3.md
- FBMN with OpenMS: featurebasedmolecularnetworking-with-openms.md
- FBMN with MetaboScape: featurebasedmolecularnetworking-with-metaboscape.md
- FBMN with Progenesis QI: featurebasedmolecularnetworking-with-progenesisQI.md
- FBMN with mzTab-M: featurebasedmolecularnetworking-with-mztab-m.md
- FBMN export to Cytoscape: featurebasedmolecularnetworking-cytoscape.md
- FBMN - Ion Identity Networking:
- IIN Workflow: fbmn-iin.md
- IIN with MZmine2: fbmn-iin-mzmine.md
- IIN with XCMS: fbmn-iin-xcms.md
- IIN with MS-DIAL: fbmn-iin-msdial.md
- MS2LDA and MotifDB Substructure Discovery: ms2lda.md
- Molecular Networking in Cytoscape: cytoscape.md
- DEREPLICATOR: dereplicator.md
- DEREPLICATOR+: dereplicator+.md
- MolDiscovery: molDiscovery.md
- Network Annotation Propagation (NAP): nap.md
- MS2LDA and MotifDB Substructure Discovery: ms2lda.md
- MolNetEnhancer: molnetenhancer.md
- MetaMiner: metaminer.md
- Sirius: sirius.md
# CycloNovo: cyclonovo.md
- Reanalysis of Data User Interface (ReDU): ReDU.md
- Qemistree: qemistree.md
- MMVEC: mmvec.md
- Merge Network Polarity: mergepolarity.md
- Chemical Directionality: chemdir.md
- Spectral Libraries:
- Libraries List: gnpslibraries.md
- Browsing Reference Spectral Libraries: browselibraries.md
- Add/Curate Reference Spectrum in the Library: spectrumcuration.md
- Reference Spectral Library Batch Addition: batchupload.md
- Reference Spectral Library mzVault Addition: batchuploadmzvault.md
- Downloading Reference Spectral Libraries: downloadlibraries.md
- Open-source Method for Reference Library Generation:
- MSMS-Chooser Workflow: msmschooser.md
- Computational Data Acquisition Prep: msmschooserdataacquisitioncomputational.md
- Data Acqusition - Thermo QExactive (v1.0): msmschooserdataacquisitionQE.md
- GNPS Tag Contribution and Analyses: tag_info.md
- Create a Public Datasets:
- Dataset Creation/Sharing: datasets.md
- Continuous Identification: continuousid.md
- Molecule Explorer: moleculeexplorer.md
- Community/Social Features:
- User Page: user.md
- Troubleshooting: troubleshooting.md
- Tutorial Guides:
- Molecular Networking - Analog Discovery in Microbial Extracts: tutorials/bacterianetworking.md
- Feature-Based Molecular Networking (FBMN) with MZmine2 - Microbiome Molecules in Fecal Samples in American Gut Project: tutorials/americangutmzmine.md
- FBMN with MS-DIAL - Microbiome Molecules in Fecal Samples in American Gut Project: tutorials/americangut-ms-dial.md
- FBMN with MetaboScape - Coffee Analysis: tutorials/coffee-tutorial-metaboscape.md
- FBMN analysis at GNPS: tutorials/featurebasedgnps.md
- Reference Data Driven Analysis: tutorials/rdd.md
- Change Log: changelog.md
- Join the GNPS community: gnps_community.md
- GNPS Workshops/Training: workshops.md
- GNPS Logos: logos.md
- Contact/Office Hours: contact.md
- GNPS Tool Index: toolindex.md
- API: api.md
- For Developers: developers.md
theme:
name: material
plugins:
- search
- git-authors:
show_contribution: true
- git-revision-date-localized:
type: datetime
- mermaid2
markdown_extensions:
- toc:
permalink: true
- admonition
- 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:pymdownx.emoji.twemoji
emoji_generator: !!python/name:pymdownx.emoji.to_svg
extra:
analytics:
provider: google
property: UA-8412213-5