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GNPS Tool Index

This is a global tool index for GNPS. Throughout this documentation we have very detailed information for how to use way more tools than we though we'd have, but its a good problem to have!

However, we recognize it might be difficult for people to simply see what all is availble in GNPS as tool and web services. This table is always evolving and hope to make it easier for people to navigate.

Please help us fill in more completely!

GNPS Workflows

Category Workflow GNPS Link Beta Link Documentation Source Code Citation
Networking Molecular Networking Workflow Workflow Documentation Github Citation
Networking Feature-Based Molecular Networking Workflow Workflow Documentation
Networking Merge Polarity Networks Workflow Workflow Documentation
Networking MS2LDA Motif DB Workflow Workflow Documentation Github-ms2lda, Github-ms2ldaviz Citation-ms2lda, Citation-ms2ldaviz
Networking MolNetEnhancer / MetaboDistTree Workflow Workflow Documentation Github-MolNetEnhancer, Github-MetaboDistTrees Citation
Data Analysis MASST Workflow Workflow Documentation --- Citation
Data Analysis Microbiome-Metabolomics Association - mmvec Workflow - Inactive Workflow ---
Annotation Large Scale Library Search Workflow Workflow ---
Annotation Library Search/Molecular Networking GC Workflow Workflow
Annotation Network Annotation Propogation (NAP) Workflow --- Documentation GitHub Citation
Annotation Sirius - Bocker Lab Workflow Workflow
Annotation Qemistree Workflow Workflow
Annotation Dereplicator Workflow ---
Annotation Dereplicator+ Workflow ---
Annotation MetaMiner --- --- Documentation --- Citation
Data Processing MSHub-GC Deconvolution Workflow Workflow
Data Processing OpenMS Feature Detector for FBMN - Future Feature Workflow Workflow ---
Data Processing LC - MZMine2 Workflow Workflow
Data Processing MSMS-Chooser Workflow Workflow Documentation Github Citation
Data Processing ChemDir Workflow --- Documentation --- ---

GNPS Web Tools

These are web tools that is run by the GNPS team and provides complementary funcationality to GNPS.

Tool Documentation Source Code Citation
ReDU Documentation GitHub Citation
GNPS Structure Server Structure processing worker TODO!
GNPS Quickstart/Batch Validator TODO TODO
GNPS Cytoscape TODO TODO
GNPS MASST Documentation TODO Citation
Metabolomics Spectrum Resolver --- GitHub TODO
Qemistree Dashboard Documentation TODO
GNPS Networking URL Formatter --- TODO
GNPS Task Esquisse Server (Beta) --- TODO
GNPS Result View Esquisse Server (Super Beta) --- TODO
GNPS Text Esquisse Server (Super Beta) --- TODO
GNPS Library Dash Explorer --- TODO
GNPS Mass Spec Calculator (Beta) --- TODO
GNPS Usage Stats Dashboard --- GitHub ---
GNPS Upset Plot Dashboard (Beta) --- GitHub ---
NP Classifier --- GitHub
GNPS LCMS Explorer --- ---
GNPS FBMN Box Plotting Dashboard --- ---

GNPS Jupyter Notebooks

These are Jupyter Notebooks that interact with GNPS web resources and do further processing. They serve as a prototype for future built-in infrastructure, check it out!

Tool Documentation Source Code Binder Launch
GNPS MASST Post Processing TODO GitHub Binder
GNPS Bioactive Molecular Networks TODO GitHub Binder

Community Tools GNPS Interfaces with

Tool Publication
MS2LDA.org Citation
NPAtlas Citation
MIBiG Citation
ClassyFire Citation
SMART NMR Citation
MassBank Citation
Cytoscape Citation
ProteoWizard Citation

GNPS Tools Interoperability Graph

Page Contributors

Ming Wang (81.32%), alan-jarmusch (16.48%), Madeleine Ernst (2.2%)


Last update: September 4, 2020 18:42:58