Science Score: 36.0%
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Low similarity (12.6%) to scientific vocabulary
Keywords
Repository
Exhaustive Formula Annotation from ions to formula
Basic Info
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
IDSL.UFAx
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exhaustive Ultra Formula Annotation (UFAx) by the Integrated Data Science Laboratory for Metabolomics and Exposomics (IDSL.ME) is an R package to annotate a number of peaks from the IDSL.IPA peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Si, N, H, As, F, I, Na, O, and P.
Table of Contents
Ultra eXhaustive Enumeration
IDSL.UFAx applies a hursitic approach to enumerate vast chemical spaces (<1027 molecular formulas). Although the IDSL.UFAx approach is computationally expensive, it is very suitable for elemental composition of unknown chromatographic peaks when the chemical space is unidentifiable. The IDSL.UFAx enumeration approach is a controlled combinatorial explosion to find molecular formulas for chromatographic peaks that were left un-assigned by a molecular formula source and enumerated chemical space approaches embedded in the IDSL.UFA package. IDSL.UFAx utilizes combinatorial subset sum solutions using 15 selected atoms for one m/z value. However, depending on the complexity of the assigned chemical space, IDSL.UFAx may be slow and should only be used for one file at a time.
Installation
install.packages("IDSL.UFAx")
Note: The IDSL.UFAx package has dependencies on RcppAlgos and gmp R packages. In some instance to install these two packages, you may need to run the following command on a linux terminal.
sudo apt-get install libgmp-dev
Workflow
To annotate your mass spectrometry data (mzXML, mzML, netCDF), mass spectrometry data should be processed using the IDSL.IPA workflow to acquire chromatographic information of the peaks (m/z-RT). When the chromatographic information of individual peaklists were generated using the IDSL.IPA workflow, download the UFAx parameter spreadsheet and select the parameters accordingly and then use this spreadsheet as the input for the IDSL.UFAx workflow:
library(IDSL.UFAx)
UFAx_workflow("Address of the UFAx parameter spreadsheet")
Wiki
Citation
[1] Fakouri Baygi, S., Banerjee S. K., Chakraborty P., Kumar, Y. Barupal, D.K. IDSL.UFA assigns high confidence molecular formula annotations for untargeted LC/HRMS datasets in metabolomics and exposomics. Analytical Chemistry, 2022, 94(39), 1331513322.
[2] Fakouri Baygi, S., Kumar, Y. Barupal, D.K. IDSL. IPA characterizes the organic chemical space in untargeted LC/HRMS datasets. Journal of proteome research, 2022, 21(6), 1485-1494.
Owner
- Name: Integrated Data Science Laboratory for Metabolomics and Exposomics
- Login: idslme
- Kind: organization
- Location: New York
- Website: www.idsl.me
- Repositories: 15
- Profile: https://github.com/idslme
GitHub Events
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Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Sadjad F Baygi | s****r@g****m | 44 |
| Dinesh Barupal | b****l@g****m | 1 |
| Sadjad Fakouri Baygi | 6****b | 1 |
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Last synced: 10 months ago
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- Total pull requests: 0
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- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
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- Bot pull requests: 0
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- Issues: 0
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Packages
- Total packages: 1
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Total downloads:
- cran 192 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 12
- Total maintainers: 1
cran.r-project.org: IDSL.UFAx
Exhaustive Chemical Enumeration for United Formula Annotation
- Homepage: https://github.com/idslme/idsl.ufax
- Documentation: http://cran.r-project.org/web/packages/IDSL.UFAx/IDSL.UFAx.pdf
- License: MIT + file LICENSE
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Latest release: 1.9.1
published about 3 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0 depends
- IDSL.IPA >= 1.7 imports
- IDSL.MXP >= 1.4 imports
- IDSL.UFA >= 1.4 imports
- RNetCDF * imports
- RcppAlgos * imports
- base64enc * imports
- doParallel * imports
- foreach * imports
- parallel * imports
- readxl * imports
- stats * imports
- xml2 * imports