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Jan Stanstrup

@janstanstrup.bsky.social
277 followers 64 following 3 posts

Assistant professor, data manager, #metabolomics octopus, data juggler, #rstats enthusiast

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Reposted by Jan Stanstrup
Steffen Neumann @sneumann.bsky.social · 08/12/2025
Out now! xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem doi.org/10.1021/acs.... with Phillipine and @jorainer.bsky.social (EURAC), @metabomichael.bsky.social, Hendrik and Norman from @ipbhalle.bsky.social, @janstanstrup.bsky.social, et al.
doi.org
xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem
High-quality data preprocessing is essential for untargeted metabolomics experiments, where increasing data set scale and complexity demand adaptable, robust, and reproducible software solutions. Modern preprocessing tools must evolve to integrate seamlessly with downstream analysis platforms, ensuring efficient and streamlined workflows. Since its introduction in 2005, the xcms R package has become one of the most widely used tools for LC-MS data preprocessing. Developed through an open-source, community-driven approach, xcms maintains long-term stability while continuously expanding its capabilities and accessibility. We present recent advancements that position xcms as a central component of a modular and interoperable software ecosystem for metabolomics data analysis. Key improvements include enhanced scalability, enabling the processing of large-scale experiments with thousands of samples on standard computing hardware. These developments empower users to build comprehensive, customizable, and reproducible workflows tailored to diverse experimental designs and analytical needs. An expanding collection of tutorials, documentation, and teaching materials further supports both new and experienced users in leveraging broader R and Bioconductor ecosystems. These resources facilitate the integration of statistical modeling, visualization tools, and domain-specific packages, extending the reach and impact of xcms workflows. Together, these enhancements solidify xcms as a cornerstone of modern metabolomics research.
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Reposted by Jan Stanstrup
Florian Huber @me-datapoint.bsky.social · 26/06/2025
@jorainer.bsky.social and @philouail.bsky.social gave a great overview of the ecosystem around #RforMassSpectrometry and #XCMS! #MetSoc25 I am super glad they now also provide options to combine with #Python and #matchms (thanks🙏)
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Henrik M. Roager @hroager.bsky.social · 26/06/2025
Our protocol paper describing our 🤱🏼MOTILITY Mother-Child Cohort: a Danish prospective longitudinal cohort study of the #infant gut #microbiome, nutrition and bowel habits has been published ✨ bmjopen.bmj.com/content/15/6/e… Thanks to Independent Research Fund Denmark for supporting our work 🙏
bmjopen.bmj.com
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Reposted by Jan Stanstrup
Johannes Rainer @jorainer.bsky.social · 25/06/2025
Steffen @sneumann.bsky.social on the history and background of @bioconductor.bsky.social during his keynote talk at the #MetSoc2025 conference 😎
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Reposted by Jan Stanstrup
Johannes Rainer @jorainer.bsky.social · 26/06/2025
Philippine @philouail.bsky.social presenting #xcms , summary of 20 years development and recent extensions at the #MetSoc2025 conference! #ProudPI 😎 #rstats @bioconductor.bsky.social #metabolomics #MassSpectrometry
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Jan Stanstrup @janstanstrup.bsky.social · 09/01/2025
so how's your day going?
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Reposted by Jan Stanstrup
ChemRxiv Bot @chemrxivbot.bsky.social · 23/12/2024
Times are changing but order matters: Transferable prediction of small molecule liquid chromatography retention times Authors: Fleming Kretschmer, Eva-Maria Harrieder, Michael Witting, Sebastian Böcker DOI: 10.26434/chemrxiv-2024-wd5j8
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Jan Stanstrup @janstanstrup.bsky.social · 19/12/2024
PhD course: Introduction to Nutritional Metabolomics The course goes through all stages of an LC-MS based untargeted metabolomics study including sample handling, pre-processing, statistics and identification. June 30th – July 4th, 2025 in Copenhagen phdcourses.ku.dk/DetailKursus... #Metabolomics
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Reposted by Jan Stanstrup
Henrik M. Roager @hroager.bsky.social · 24/11/2024
📣 Do you know an expert in analytical chemistry and #metabolomics 🌟 that would be excited about supporting cutting-edge research within the fields of #nutrition, #microbiome and health? (help us - retweet and like) 🙏 📍 Copenhagen ✉ Deadline: 12 January 2025 🌞 employment.ku.dk/staff/?show=...
jobportal.ku.dk
Metabolomics Platform Manager
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Reposted by Jan Stanstrup
Henrik M. Roager @hroager.bsky.social · 24/11/2024
📣 A 3-year #postdoc position in #Metabolomics, Microbiome, and Cardiometabolic health is now available in our group in #Copenhagen 🌟 Do you know a bright, kind and motivated candidate? (help us share, like) 🙏 ❤️ ✉ Deadline: 5 January 2025 🌞 employment.ku.dk/faculty/?sho...
employment.ku.dk
Postdoc in Metabolomics, Microbiome, and Cardiometabolic health
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