IonFlow: a galaxy tool for the analysis of ionomics data sets.
Galaxy platform
Ionomics
Network biology
Journal
Metabolomics : Official journal of the Metabolomic Society
ISSN: 1573-3890
Titre abrégé: Metabolomics
Pays: United States
ID NLM: 101274889
Informations de publication
Date de publication:
25 09 2021
25 09 2021
Historique:
received:
09
05
2021
accepted:
13
09
2021
entrez:
25
9
2021
pubmed:
26
9
2021
medline:
19
1
2022
Statut:
epublish
Résumé
Inductively coupled plasma mass spectrometry (ICP-MS) experiments generate complex multi-dimensional data sets that require specialist data analysis tools. Here we describe tools to facilitate analysis of the ionome composed of high-throughput elemental profiling data. IonFlow is a Galaxy tool written in R for ionomics data analysis and is freely accessible at https://github.com/wanchanglin/ionflow . It is designed as a pipeline that can process raw data to enable exploration and interpretation using multivariate statistical techniques and network-based algorithms, including principal components analysis, hierarchical clustering, relevance network extraction and analysis, and gene set enrichment analysis. The pipeline is described and tested on two benchmark data sets of the haploid S. Cerevisiae ionome and of the human HeLa cell ionome.
Identifiants
pubmed: 34562172
doi: 10.1007/s11306-021-01841-z
pii: 10.1007/s11306-021-01841-z
pmc: PMC8464566
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
91Subventions
Organisme : Medical Research Council
ID : MR/P011705/2
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/P011705/1
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 202952/D/16/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UP_A090_1006
Pays : United Kingdom
Informations de copyright
© 2021. The Author(s).
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