Mercurial > repos > recetox > ramclustr

annotate test-data/test4_metadata_csv_2.txt @ 4:69e0da4703b5 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
author recetox
date Fri, 04 Feb 2022 08:31:26 +0000
parents 15e173c5762c
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15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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1 Raw mass spectrometry data were processed using an R based workflow for feature detection, retention time alignment, feature grouping, peak filling, feature clustering. Feature data was input as .csv files with ramclustR parameter settings of st = 1 sr = 0.5 and maxt = 60.RAMClustR (version 1.2.2) was utilized to cluster features into spectra (Broeckling 2014). The feature similarity matrix was clustered using fastcluster package heirarchical clustering method using the average method. The dendrogram was cut using the cutreeDynamicTree function from the dynamicTreeCut package. Cutting parameters were set to minModuleSize = 2, hmax = 0.3, and deepSplit = FALSE.
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
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3 203 features were collapsed into 38 spectra. Since there were fewer than five injections, clustering was performed only using retention time simiilarity.
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
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15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
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5 (Broeckling 2014): Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014. 86(14):6812-7.
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
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