Databases, softwares and tools

1. SOFTWARES

META-ANALYSIS

1.1 Amanida tool

for the meta-analysis of non-integral data (p-values and fold-changes/trends) for any OMICS.
Github Amanida or CRAN.

–> Quantitative analysis (volcano plots) or Qualitative analysis (vote counting and explore plots)

Please cite:
Llambrich M, Correig E, Gumà J, Brezmes J, Cumeras R. Amanida: An R package for meta-analysis of metabolomics non-integral data. Bioinformatics 2022, 38(2):583-585, doi: 10.1093/bioinformatics/btab591.

Registered design:
Maria Llambrich. Design registered at SafeCreative w/ reference 2111229876715 (Nov 22, 2021).

1.2. Easy-Amanida tool

Harmonize, Analyze, Discover: Easy-Amanida Simplifies Metabolomics Meta-Analysis.

Github Easy-Amanida (with the link to the R Shiny app):
https://brui.shinyapps.io/easy-amanida/

  • Meta-Analysis: Easy-Amanida enables users to perform meta-analyses by combining aggregate statistical data from multiple metabolomics studies.
  • Data Harmonization: The tool addresses the challenge of compound naming harmonization, which is a common issue in metabolomics. It can convert compound names to a unique identifier (InChIKey) using the Webchem package, ensuring consistency and accuracy in the analysis.
    • it can also be used with other OMICS without selecting the data harmonization tab
  • User-Friendly Interface: Easy-Amanida is implemented as a Shiny web app, making it accessible to researchers without extensive programming skills. Users can easily upload their datasets and choose between quantitative and qualitative analysis modes.
  • Visualizations: The tool provides various visualizations of the results, including volcano plots for quantitative analysis and vote-counting and explore plots for qualitative analysis. These visualizations help users interpret and understand the data.
  • Customization: Users can customize analysis parameters, such as significance thresholds, to suit their specific research needs.

Please cite:
Llambrich M, Satorra P, Correig E, Gumà J, Brezmes J, Tebé C, Cumeras R. Easy-Amanida: An R Shiny application for the meta-analysis of aggregate results in clinical metabolomics using Amanida and Webchem. Res Synth Methods. 2024 Mar 13:e1713. doi: 10.1002/jrsm.1713. Epub ahead of print. PMID: 38480474.

Tutorial and Use Case:

Easy-Amanida Tutorial and Use Case

METABOLOMICS ANALYSIS

1.3 GcDuo

the first open soucre full workflow for GCxGC data (from raw data to peak table)

Please cite:
Llambrich M, Brezmes J, Cumeras R. Pre-processing algorithm for GCxGC-MS raw data registered at Safe Creative w/ reference 2205241209139 (May 24, 2022).

ChrTOF is ChromaTOF gold standard software. BM is a mixture of reference standards of compounds found in breath.



Registered design:
Raquel Cumeras. Design registered at BOIP w/reference 87508-01 (May 3, 2018).

2. TOOLS

METABOLITES NAMING HARMONIZATION

2.1 Metabolites Merging Strategy

A systematic framework to harmonize multiple metabolite datasets for enhanced interstudy comparability in just three steps.

Please cite:
Villalba H, Llambrich M, Gumà J, Brezmes J, Cumeras R. A Metabolites Merging Strategy (MMS): Harmonization to Enable Studies’ Intercomparison. Metabolites. 2023 Nov 21;13(12):1167. doi: 10.3390/metabo13121167. PMID: 38132849; PMCID: PMC10744506.

3. DATABASES

BIOFLUIDS COMPOSITION

3.1 Life Fluids database

the first multiomics database of human biofluids including metabolites, proteins + associated genes, transcripts, and chemical elements.

https://lifefluids.com/composition

* indicates ongoing manual curation

Please cite:
Life Fluids 1 (urine): Villalba H, Llambrich M, Cumeras R. “BBDD Life Fluids Urine” registered at SafeCreative w/
reference 2206081328615 (June 8, 2022).
Life Fluids 2 (saliva and breath): Romera P, Villalba H, Llambrich M, Cumeras R. “Human biofluids composition: saliva
and breath as life fluids” registered at SafeCreative w/ reference 2306124568135 (June 16, 2023).
Life Fluids 3 (blood): Bordoy P, Villalba H, Llambrich M, R. Cumeras R. “Human blood metabolome complete database”
registered at SafeCreative w/ reference 2401196709377 (January 19, 2024).

Registered designs:
– Héctor Villalba, Raquel Cumeras. Design registered at SafeCreative w/ reference 2206131358555 (Jun 13, 2022).
– Maria Llambrich. Design registered at SafeCreative w/reference 2110269633500 (Oct 26, 2021).

3.2 Urine Volatilome database

Volatiles found in human urine with headspace techniques coupled to gas chromatography – mass spectrometry.

DOWNLOAD it here: https://doi.org/10.5281/zenodo.6883341

Please cite:
Llambrich M, Brezmes J, Cumeras R. The untargeted urine volatilome for biomedical applications: methodology and volatilome database. Biol Proced Online. 2022 Dec 1;24(1):20. doi: 10.1186/s12575-022-00184-w. PMID: 36456991.