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WOMBAT-P : Benchmar...
WOMBAT-P : Benchmarking Label-Free Proteomics Data Analysis Workflows
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- Bouyssié, David (författare)
- Université Paul Sabatier
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- Altıner, Pınar (författare)
- Université Paul Sabatier
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- Capella-Gutierrez, Salvador (författare)
- Centro Nacional de Supercomputación
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- Fernández, José M. (författare)
- Centro Nacional de Supercomputación
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- Hagemeijer, Yanick Paco (författare)
- University of Groningen,University Medical Center Groningen
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- Horvatovich, Peter (författare)
- University of Groningen
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- Hubálek, Martin (författare)
- Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic
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- Levander, Fredrik (författare)
- Lund University,Lunds universitet,Institutionen för immunteknologi,Institutioner vid LTH,Lunds Tekniska Högskola,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Department of Immunotechnology,Departments at LTH,Faculty of Engineering, LTH,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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- Mauri, Pierluigi (författare)
- CNR Institute for Biomedical Technologies (ITB-CNR)
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- Palmblad, Magnus (författare)
- Leiden University Medical Centre
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- Raffelsberger, Wolfgang (författare)
- University of Strasbourg
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- Rodríguez-Navas, Laura (författare)
- Centro Nacional de Supercomputación
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- Di Silvestre, Dario (författare)
- CNR Institute for Biomedical Technologies (ITB-CNR)
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- Kunkli, Balázs Tibor (författare)
- University of Debrecen
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- Uszkoreit, Julian (författare)
- Ruhr-University Bochum
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- Vandenbrouck, Yves (författare)
- French Alternative Energies and Atomic Energy Commission (CEA)
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- Vizcaíno, Juan Antonio (författare)
- Wellcome Trust
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Winkelhardt, Dirk (författare)
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- Schwämmle, Veit (författare)
- University of Southern Denmark
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(creator_code:org_t)
- 2024
- 2024
- Engelska 12 s.
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Ingår i: Journal of Proteome Research. - 1535-3893. ; 23:1, s. 418-429
- Relaterad länk:
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http://dx.doi.org/10...
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines.
Ämnesord
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- benchmarking
- data analysis
- label-free proteomics
- quality metrics
- workflow
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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Till lärosätets databas
- Av författaren/redakt...
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Bouyssié, David
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Altıner, Pınar
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Capella-Gutierre ...
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Fernández, José ...
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Hagemeijer, Yani ...
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Horvatovich, Pet ...
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visa fler...
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Hubálek, Martin
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Levander, Fredri ...
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Mauri, Pierluigi
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Palmblad, Magnus
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Raffelsberger, W ...
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Rodríguez-Navas, ...
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Di Silvestre, Da ...
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Kunkli, Balázs T ...
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Uszkoreit, Julia ...
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Vandenbrouck, Yv ...
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Vizcaíno, Juan A ...
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Winkelhardt, Dir ...
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Schwämmle, Veit
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- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Data och informa ...
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och Bioinformatik
- Artiklar i publikationen
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Journal of Prote ...
- Av lärosätet
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Lunds universitet