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Biotite: new tools for a versatile Python bioinformatics library
Kunzmann, Patrick, Müller, Tom David, Greil, Maximilian, Krumbach, Jan Hendrik, Anter, Jacob Marcel, Bauer, Daniel, Islam, Faisal, Hamacher, Kay
Published in BMC bioinformatics (05.06.2023)
Published in BMC bioinformatics (05.06.2023)
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Journal Article
Correct orchestration of federated learning generic algorithms: Python translation to CSP and verification by PAT
Djukic, Miodrag, Prokić, Ivan, Popovic, Miroslav, Ghilezan, Silvia, Popovic, Marko, Prokić, Simona
Published in International journal on software tools for technology transfer (01.02.2025)
Published in International journal on software tools for technology transfer (01.02.2025)
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Journal Article
PyNoetic: A modular python framework for no-code development of EEG brain-computer interfaces
Singh, Gursimran, Chharia, Aviral, Upadhyay, Rahul, Kumar, Vinay, Longo, Luca
Published in PloS one (06.08.2025)
Published in PloS one (06.08.2025)
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Journal Article
RABiTPy: an open-source Python software for rapid, AI-powered bacterial tracking and analysis
Sen, Samyabrata, Vairagare, Indraneel, Gosai, Jitendrapuri, Shrivastava, Abhishek
Published in BMC bioinformatics (18.05.2025)
Published in BMC bioinformatics (18.05.2025)
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Journal Article
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS
Johnson, Jeanette A. I., Tsang, Ashley P., Mitchell, Jacob T., Zhou, David L., Bowden, Julia, Davis-Marcisak, Emily, Sherman, Thomas, Liefeld, Ted, Loth, Melanie, Goff, Loyal A., Zimmerman, Jacquelyn W., Kinny-Köster, Ben, Jaffee, Elizabeth M., Tamayo, Pablo, Mesirov, Jill P., Reich, Michael, Fertig, Elana J., Stein-O’Brien, Genevieve L.
Published in Nature protocols (01.12.2023)
Published in Nature protocols (01.12.2023)
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Journal Article
PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data
Georgi, Benjamin, Costa, Ivan Gesteira, Schliep, Alexander
Published in BMC bioinformatics (06.01.2010)
Published in BMC bioinformatics (06.01.2010)
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Journal Article
Portable BLAST-like algorithm library and its implementations for command line, Python, and R
Schmid, Steven, Jeevannavar, Aditya, Julian, Timothy R., Tamminen, Manu
Published in PloS one (30.11.2023)
Published in PloS one (30.11.2023)
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Journal Article
PyUNIxMD: A Python‐based excited state molecular dynamics package
Lee, In Seong, Ha, Jong‐Kwon, Han, Daeho, Kim, Tae In, Moon, Sung Wook, Min, Seung Kyu
Published in Journal of computational chemistry (15.09.2021)
Published in Journal of computational chemistry (15.09.2021)
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Journal Article
Legate Sparse: Distributed Sparse Computing in Python
Yadav, Rohan, Lee, Wonchan, Elibol, Melih, Patti, Taylor Lee, Papadakis, Manolis, Garland, Michael, Aiken, Alex, Kjolstad, Fredrik, Bauer, Michael
Published in International Conference for High Performance Computing, Networking, Storage and Analysis (Online) (11.11.2023)
Published in International Conference for High Performance Computing, Networking, Storage and Analysis (Online) (11.11.2023)
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Conference Proceeding
ViSAPy: A Python tool for biophysics-based generation of virtual spiking activity for evaluation of spike-sorting algorithms
Hagen, Espen, Ness, Torbjørn V., Khosrowshahi, Amir, Sørensen, Christina, Fyhn, Marianne, Hafting, Torkel, Franke, Felix, Einevoll, Gaute T.
Published in Journal of neuroscience methods (30.04.2015)
Published in Journal of neuroscience methods (30.04.2015)
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Journal Article
OMD Curation Toolkit: a workflow for in-house curation of public omics datasets
Piquer-Esteban, Samuel, Arnau, Vicente, Diaz, Wladimiro, Moya, Andrés
Published in BMC bioinformatics (09.05.2024)
Published in BMC bioinformatics (09.05.2024)
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Journal Article
Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison
Kuijpers, Lucas, Hornung, Bastian, van den Hout - van Vroonhoven, Mirjam C. G. N., van IJcken, Wilfred F. J., Grosveld, Frank, Mulugeta, Eskeatnaf
Published in BMC genomics (12.04.2024)
Published in BMC genomics (12.04.2024)
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Journal Article
Bioinformatic pipelines in Python with Leaf
Napolitano, Francesco, Mariani-Costantini, Renato, Tagliaferri, Roberto
Published in BMC bioinformatics (21.06.2013)
Published in BMC bioinformatics (21.06.2013)
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Journal Article