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plantR: An R package and workflow for managing species records from biological collections2021 Methods in Ecology and Evolution article Computer Science Research Data Management Practices Open access
Renato A. Ferreira de Lima, Andrea Sánchez‐Tapia, Sara Ribeiro Mortara, Hans ter Steege, Marinez Ferreira de Siqueira
40citations -
plantR: An R package and workflow for managing species records from biological collections2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Research Data Management Practices Open access
Renato A. Ferreira de Lima, Andrea Sánchez‐Tapia, Sara Ribeiro Mortara, Hans ter Steege, Marinez Ferreira de Siqueira
10citations -
A Comprehensive Workflow for Applying Single-Cell Clustering and Pseudotime Analysis to Flow Cytometry Data2020 The Journal of Immunology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Janine E. Melsen, Monique M. van Ostaijen-ten Dam, Arjan C. Lankester, Marco W. Schilham, Erik B. van den Akker
56citations -
MeDUSA: Taming your metabolic data sets using an R-package for data processing of Direct Infusion Untargeted Single-Cell Analysis0citations
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MeDUSA: Taming your metabolic data sets using an R-package for data processing of Direct Infusion Untargeted Single-Cell Analysis0citations
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A data reduction workflow for mass spectrometry proteoform testing in the clinical laboratory: from antithrombin peaks to diagnosis2026 Clinical Chemistry and Laboratory Medicine (CCLM) article Chemistry Advanced Proteomics Techniques and Applications Open access
Mirjam Kruijt, María Eugenia de la Morena‐Barrio, Javier Corral, Christa M. Cobbaert, L. Renee Ruhaak
0citations -
A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object2022 Research Ideas and Outcomes article Decision Sciences Scientific Computing and Data Management Open access
Anna Niehues, Casper de Visser, Fiona A. Hagenbeek, Naama Karu, Alida S. D. Kindt, Purva Kulkarni, +5 more
1citations -
A Workflow for Missing Values Imputation of Untargeted Metabolomics Data2020 Metabolites article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
Tariq O. Faquih, Maarten van Smeden, Jiao Min Luo, Saskia le Cessie, Gabi Kastenmüller, Jan Krumsiek, +6 more
53citations -
Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images2024 Computer Methods and Programs in Biomedicine article Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Johannes Raufeisen, Kunpeng Xie, Fabian Hörst, Till A. Braunschweig, Jianning Li, Jens Kleesiek, +6 more
11citations -
EchoGO: cross-species consensus enrichment for transcriptomic interpretation2026 Zenodo (CERN European Organization for Nuclear Research) software Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Camilo Escobar-Sierra, Felix Langschied, Angelina Miller, Pedro A. Inostroza
0citations -
Bridging HPC Communities through the Julia Programming Language2022 arXiv (Cornell University) preprint Computer Science Parallel Computing and Optimization Techniques Open access
Valentin Churavy, William F. Godoy, Carsten Bauer, Hendrik Ranocha, Michael Schlottke‐Lakemper, Ludovic Räss, +6 more
18citations -
QSP Designer: Quantitative systems pharmacology modeling with modular biological process map notation and multiple language code generation2023 CPT Pharmacometrics & Systems Pharmacology article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
David M. Hollinshead, Piet H. van der Graaf, Andrzej M. Kierzek
14citations -
GlycoDash: automated, visually assisted curation of glycoproteomics datasets for large sample numbers2025 Analytical and Bioanalytical Chemistry article Biochemistry, Genetics and Molecular Biology Glycosylation and Glycoproteins Research Open access
Tamás Pongrácz, Steinar Gijze, Agnes L. Hipgrave Ederveen, Rico J. E. Derks, David Falck
5citations -
A system for independent evaluation of clinical prediction models while preserving intellectual property and data privacy2026 Zenodo (CERN European Organization for Nuclear Research) preprint Mathematics Statistical Methods in Epidemiology Open access
Joie Ensor, Ben Van Calster, Lasai Barreñada, Laure Wynants, Benjamin I. Perry
0citations