Back

A new workflow combining R packages for statistical analysis of metabolites

Ferrario, P. G.

2019-11-28 bioinformatics
10.1101/848812 bioRxiv
Show abstract

In metabolomics, the investigation of an association between many metabolites and one trait (such as age in humans or cultivar in foods) is a central research question. On this topic, we present a complete statistical analysis, combining selected R packages in a new workflow, which we are sharing completely, according to modern standards and research reproducibility requirements. We demonstrate the workflow using a large-scale study with public data, available on repositories. Hence, the workflow can directly be re-used on quite different metabolomics data, when searching for association with one covariate of interest.

Matching journals

The top 3 journals account for 50% of the predicted probability mass.

1
Metabolites
50 papers in training set
Top 0.1%
26.1%
2
BMC Bioinformatics
383 papers in training set
Top 0.3%
18.8%
3
Bioinformatics
1061 papers in training set
Top 3%
8.5%
50% of probability mass above
4
Peer Community Journal
254 papers in training set
Top 0.4%
6.4%
5
PLOS Computational Biology
1633 papers in training set
Top 5%
6.4%
6
PLOS ONE
4510 papers in training set
Top 39%
3.6%
7
Briefings in Bioinformatics
326 papers in training set
Top 3%
2.6%
8
Nature Communications
4913 papers in training set
Top 45%
2.5%
9
Methods in Ecology and Evolution
160 papers in training set
Top 1%
2.4%
10
Bioinformatics Advances
184 papers in training set
Top 2%
2.1%
11
Genomics, Proteomics & Bioinformatics
171 papers in training set
Top 3%
1.7%
12
NAR Genomics and Bioinformatics
214 papers in training set
Top 3%
1.2%
13
Scientific Reports
3102 papers in training set
Top 66%
1.2%
14
SoftwareX
15 papers in training set
Top 0.3%
1.0%
15
Computational and Structural Biotechnology Journal
216 papers in training set
Top 7%
0.9%
16
Analytical Chemistry
205 papers in training set
Top 2%
0.8%
17
BMC Genomics
328 papers in training set
Top 6%
0.8%
18
GigaScience
172 papers in training set
Top 3%
0.8%
19
PeerJ
261 papers in training set
Top 16%
0.7%
20
Journal of Proteome Research
215 papers in training set
Top 2%
0.7%
21
Database
51 papers in training set
Top 1%
0.6%
22
Nature Protocols
30 papers in training set
Top 0.4%
0.5%
23
International Journal of Molecular Sciences
453 papers in training set
Top 19%
0.5%
24
npj Systems Biology and Applications
99 papers in training set
Top 3%
0.5%
25
Molecular & Cellular Proteomics
158 papers in training set
Top 2%
0.5%
26
Nucleic Acids Research
1128 papers in training set
Top 21%
0.5%