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Pace-Loscos T, Gal J, Contu S, Schiappa R, Chamorey E, Culié D. StatiCAL: an interactive tool for statistical analysis of biomedical data and scientific valorization. BMC Bioinformatics 2024; 25:210. [PMID: 38867185 PMCID: PMC11167775 DOI: 10.1186/s12859-024-05829-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND In the realm of biomedical research, the growing volume, diversity and quantity of data has escalated the demand for statistical analysis as it is indispensable for synthesizing, interpreting, and publishing data. Hence the need for accessible analysis tools drastically increased. StatiCAL emerges as a user-friendly solution, enabling researchers to conduct basic analyses without necessitating extensive programming expertise. RESULTS StatiCAL includes divers functionalities: data management, visualization on variables and statistical analysis. Data management functionalities allow the user to freely add or remove variables, to select sub-population and to visualise selected data to better perform the analysis. With this tool, users can freely perform statistical analysis such as descriptive, graphical, univariate, and multivariate analysis. All of this can be performed without the need to learn R coding as the software is a graphical user interface where all the action can be performed by clicking a button. CONCLUSIONS StatiCAL represents a valuable contribution to the field of biomedical research. By being open-access and by providing an intuitive interface with robust features, StatiCAL allow researchers to gain autonomy in conducting their projects.
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Affiliation(s)
- Tanguy Pace-Loscos
- Département d'Epidémiologie, de Biostatistique et des Données de Santé, Centre Antoine Lacassagne, Université Cote d'Azur, Nice, France.
| | - Jocelyn Gal
- Département d'Epidémiologie, de Biostatistique et des Données de Santé, Centre Antoine Lacassagne, Université Cote d'Azur, Nice, France
| | - Sara Contu
- Département d'Epidémiologie, de Biostatistique et des Données de Santé, Centre Antoine Lacassagne, Université Cote d'Azur, Nice, France
| | - Renaud Schiappa
- Département d'Epidémiologie, de Biostatistique et des Données de Santé, Centre Antoine Lacassagne, Université Cote d'Azur, Nice, France
| | - Emmanuel Chamorey
- Département d'Epidémiologie, de Biostatistique et des Données de Santé, Centre Antoine Lacassagne, Université Cote d'Azur, Nice, France
| | - Dorian Culié
- Institut Universitaire de la Face et du Cou, Centre Antoine Lacassagne, Département de Chirurgie Cervico-Faciale, Université Cote d'Azur, 06103, Nice, France
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Eiteneuer C, Velasco D, Atemia J, Wang D, Schwacke R, Wahl V, Schrader A, Reimer JJ, Fahrner S, Pieruschka R, Schurr U, Usadel B, Hallab A. GXP: Analyze and Plot Plant Omics Data in Web Browsers. PLANTS 2022; 11:plants11060745. [PMID: 35336631 PMCID: PMC8952246 DOI: 10.3390/plants11060745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/15/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
Abstract
Next-generation sequencing and metabolomics have become very cost and work efficient and are integrated into an ever-growing number of life science research projects. Typically, established software pipelines analyze raw data and produce quantitative data informing about gene expression or concentrations of metabolites. These results need to be visualized and further analyzed in order to support scientific hypothesis building and identification of underlying biological patterns. Some of these tools already exist, but require installation or manual programming. We developed “Gene Expression Plotter” (GXP), an RNAseq and Metabolomics data visualization and analysis tool entirely running in the user’s web browser, thus not needing any custom installation, manual programming or uploading of confidential data to third party servers. Consequently, upon receiving the bioinformatic raw data analysis of RNAseq or other omics results, GXP immediately enables the user to interact with the data according to biological questions by performing knowledge-driven, in-depth data analyses and candidate identification via visualization and data exploration. Thereby, GXP can support and accelerate complex interdisciplinary omics projects and downstream analyses. GXP offers an easy way to publish data, plots, and analysis results either as a simple exported file or as a custom website. GXP is freely available on GitHub (see introduction)
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Affiliation(s)
- Constantin Eiteneuer
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - David Velasco
- Faculty of Natural Sciences, Norges Teknisk-Naturvitenskapelige Universitet, 7034 Trondheim, Norway;
| | - Joseph Atemia
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
| | - Dan Wang
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Rainer Schwacke
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
| | - Vanessa Wahl
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany;
| | - Andrea Schrader
- Institute for Biology I, RWTH Aachen University, 52062 Aachen, Germany; (A.S.); (J.J.R.)
| | - Julia J. Reimer
- Institute for Biology I, RWTH Aachen University, 52062 Aachen, Germany; (A.S.); (J.J.R.)
- Faculty of Technology, University of Applied Science Emden/Leer, Molecular Biosciences, 26723 Emden, Germany
| | - Sven Fahrner
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Roland Pieruschka
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Ulrich Schurr
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
| | - Asis Hallab
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
- Correspondence:
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