https://github.com/jorainer/xcms-gnps-tools
Utility functions for the use of xcms with GNPS
https://github.com/jorainer/xcms-gnps-tools
Last synced: about 2 months ago
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Utility functions for the use of xcms with GNPS
- Host: GitHub
- URL: https://github.com/jorainer/xcms-gnps-tools
- Owner: jorainer
- Created: 2019-04-08T03:49:59.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2019-10-31T09:21:46.000Z (over 5 years ago)
- Last Synced: 2025-03-24T04:23:30.964Z (3 months ago)
- Language: R
- Size: 11.7 KB
- Stars: 6
- Watchers: 3
- Forks: 3
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Utility functions for use of xcms with GNPS
Authors: Johannes Rainer, Mar Garcia-Aloy and Michael Witting.
This repository contains some utility functions to integrate `xcms`-based data
processing into the GNPS [Feature-Based Molecular
Networking](https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/)
workflow (FBMN). See [this
page](https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-xcms3)
for details on xcms integration into FBMN, and the following [GitHub
repo](https://github.com/DorresteinLaboratory/XCMS3_FeatureBasedMN) for example
scripts as Jupyter notebook and RCommander script.
The main provided functions are:
- `formatSpectraForGNPS`: format spectra for MGF export in the format expected
by GNPS.
- `getEdgelist`: extract a list of *edges* between co-eluting ions potentially
representing adducts or isotopes of the same metabolite as defined by
`CAMERA`.
- `getFeatureAnnotations`: extract adduct annotations for features from a
`CAMERA` result in the format required for Ion Identity Networking (IIN) in
FBMN/GNPS.