GXP: Analyze and Plot Plant Omics Data in Web Browsers
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 concentra...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-03-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/6/745 |
| _version_ | 1797443437917634560 |
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| author | Constantin Eiteneuer David Velasco Joseph Atemia Dan Wang Rainer Schwacke Vanessa Wahl Andrea Schrader Julia J. Reimer Sven Fahrner Roland Pieruschka Ulrich Schurr Björn Usadel Asis Hallab |
| author_facet | Constantin Eiteneuer David Velasco Joseph Atemia Dan Wang Rainer Schwacke Vanessa Wahl Andrea Schrader Julia J. Reimer Sven Fahrner Roland Pieruschka Ulrich Schurr Björn Usadel Asis Hallab |
| author_sort | Constantin Eiteneuer |
| collection | DOAJ |
| description | 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) |
| first_indexed | 2024-03-09T12:56:03Z |
| format | Article |
| id | doaj.art-8b9c5785b12647a8a32bd1bd4b9ca85d |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T12:56:03Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-8b9c5785b12647a8a32bd1bd4b9ca85d2023-11-30T22:00:29ZengMDPI AGPlants2223-77472022-03-0111674510.3390/plants11060745GXP: Analyze and Plot Plant Omics Data in Web BrowsersConstantin Eiteneuer0David Velasco1Joseph Atemia2Dan Wang3Rainer Schwacke4Vanessa Wahl5Andrea Schrader6Julia J. Reimer7Sven Fahrner8Roland Pieruschka9Ulrich Schurr10Björn Usadel11Asis Hallab12IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, GermanyFaculty of Natural Sciences, Norges Teknisk-Naturvitenskapelige Universitet, 7034 Trondheim, NorwayIBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, GermanyIBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, GermanyIBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, GermanyMax Planck Institute for Molecular Plant Physiology, 14476 Potsdam, GermanyInstitute for Biology I, RWTH Aachen University, 52062 Aachen, GermanyInstitute for Biology I, RWTH Aachen University, 52062 Aachen, GermanyIBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, GermanyIBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, GermanyIBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, GermanyIBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, GermanyIBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, GermanyNext-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)https://www.mdpi.com/2223-7747/11/6/745RNA sequencingmetabolomicsdata visualizationoverrepresentation analysiscorrelationcluster analysis |
| spellingShingle | Constantin Eiteneuer David Velasco Joseph Atemia Dan Wang Rainer Schwacke Vanessa Wahl Andrea Schrader Julia J. Reimer Sven Fahrner Roland Pieruschka Ulrich Schurr Björn Usadel Asis Hallab GXP: Analyze and Plot Plant Omics Data in Web Browsers Plants RNA sequencing metabolomics data visualization overrepresentation analysis correlation cluster analysis |
| title | GXP: Analyze and Plot Plant Omics Data in Web Browsers |
| title_full | GXP: Analyze and Plot Plant Omics Data in Web Browsers |
| title_fullStr | GXP: Analyze and Plot Plant Omics Data in Web Browsers |
| title_full_unstemmed | GXP: Analyze and Plot Plant Omics Data in Web Browsers |
| title_short | GXP: Analyze and Plot Plant Omics Data in Web Browsers |
| title_sort | gxp analyze and plot plant omics data in web browsers |
| topic | RNA sequencing metabolomics data visualization overrepresentation analysis correlation cluster analysis |
| url | https://www.mdpi.com/2223-7747/11/6/745 |
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