OptiLCMS Tool for CentWave Parameter Optimization (Work in Progress) #278
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Optimize the critical parameters of peak picking and alignment for the following data processing in an automatic way.
|
The OptiLCMS package is currently available exclusively through this GitHub repository. I am currently working on creating a Conda recipe to make the package accessible and ensure the integration into Galaxy requirements. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Addition of OptiLCMS Tool for CentWave Parameter Optimization
Description
This PR introduces a new Galaxy tool called OptiLCMS, designed to automate the optimization of parameters for the CentWave algorithm. CentWave is a widely used method for peak detection and extraction in LC-MS data.
The tool utilizes the following core functions from the R package OptiLCMS:
PerformROIExtraction(): Identifies regions of interest (ROIs) in the LC-MS data for further analysis.SetPeakParam(): Configures the initial parameters for the CentWave algorithm.PerformParamsOptimization(): Executes the optimization process to refine the CentWave parameters based on the input dataset.FOR CONTRIBUTOR: