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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 -
User-friendly high-content imaging analysis on a single desktop: R package H5CellProfiler2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Cell Image Analysis Techniques Open access
Steven Wink, Gerhard A. Burger, Sylvia E. Le Dévédec, Joost B. Beltman, Bob van de Water
3citations -
DAISIEprep: an R package for the extraction and formatting of data for the island biogeography model DAISIE2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Environmental Science Ecology and Vegetation Dynamics Studies Open access
Joshua W. Lambert, Lizzie Roeble, Théo Pannetier, Rampal S. Etienne, Luís Valente
0citations -
Clusterwise Independent Component Analysis (C-Ica): An R Package for Clustering Subjects Based on Ica Patterns Underlying Three-Way (Brain) Data2024 SSRN Electronic Journal preprint Neuroscience Functional Brain Connectivity Studies Open access
Jeffrey Durieux, Serge A.R.B. Rombouts, Marisa Koini, Juan Claramunt Gonzalez, Tom F. Wilderjans
1citations -
Understanding functional consequences of type 2 diabetes risk loci using the universal data integration and visualization R package CONQUER2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Gerard A. Bouland, Joline W. J. Beulens, Joey Nap, Arno R. van der Slik, Arnaud Zaldumbide, Leen M. ‘t Hart, +1 more
1citations -
Aggregate data modelling: a fast implementation for fitting pharmacometrics models to summary-level data in R2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Mathematics Statistical Methods in Clinical Trials Open access
Hidde van de Beek, Pyry A. J. Välitalo, J. G. Coen van Hasselt, Laura B. Zwep
0citations -
The Network Zoo: a multilingual package for the inference and analysis of biological networks2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Marouen Ben Guebila, Tian Wang, Camila M. Lopes‐Ramos, Viola Fanfani, Deborah A. Weighill, Rebekka Burkholz, +17 more
1citations -
Converting networks to predictive logic models from perturbation signalling data with CellNOpt2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
Enio Gjerga, Panuwat Trairatphisan, Attila Gábor, Hermann Koch, Francesco Ceccarelli, Aurélien J. F. Dugourd, +2 more
4citations -
CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
James Shiniti Nagai, Nils B. Leimkühler, Michael T. Schaub, Rebekka K. Schneider, Ivan G. Costa
9citations -
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 -
Edna2iqi: An Edna/Random Forest-Based Prediction Tool that Accurately Predicts Ecological Status for Regulatory-Compliance2025 SSRN Electronic Journal preprint Environmental Science Environmental DNA in Biodiversity Studies Open access
Adam J. Wyness, Thorsten Stoeck, Barbara J. Morrissey, Iain K. Berrill, Connie Fairbairn, Tim Foster, +5 more
0citations -
SALTED: a symmetry-adapted machine-learning program for predicting electron-densities in molecules and materials2026 arXiv (Cornell University) preprint Materials Science Machine Learning in Materials Science Open access
Zekun Lou, Alan M. Lewis, T. Bernhard, Lukas Seifert, Agustin Salcedo, Florian Kleemiss, +2 more
0citations -
Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Environmental Science Species Distribution and Climate Change Open access
Owen G. Osborne, Henry G. Fell, Hannah Atkins, Jan van Tol, Daniel Phillips, Leonel Herrera‐Alsina, +13 more
3citations -
Plant PhysioSpace: a robust tool to compare stress response across plant species2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Ali Hadizadeh Esfahani, Janina Maß, Asis Hallab, Bernhard Schuldt, David Nevarez, Björn Usadel, +3 more
1citations -
WALDO: community-Wide Annotation of γδ Lymphocytes in single-cell Data, Openly benchmarked2026 Zenodo (CERN European Organization for Nuclear Research) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Farid Keramati, Moosa Rezwani, Likai Tan, David Hamilton, Zheng Song, Tao Yang, +10 more
0citations