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    SciPy 1.0: fundamental algorithms for scientific computing in Python
                                      
                                            Virtanen, Pauli,                              Gommers, Ralf,                              Oliphant, Travis E.,                              Haberland, Matt,                              Reddy, Tyler,                              Cournapeau, David,                              Burovski, Evgeni,                              Peterson, Pearu,                              Weckesser, Warren,                              Bright, Jonathan,                              van der Walt, Stéfan J.,                              Brett, Matthew,                              Wilson, Joshua,                              Millman, K. Jarrod,                              Mayorov, Nikolay,                              Nelson, Andrew R. J.,                              Jones, Eric,                              Kern, Robert,                              Larson, Eric,                              Carey, C J,                              Polat, İlhan,                              Feng, Yu,                              Moore, Eric W.,                              VanderPlas, Jake,                              Laxalde, Denis,                              Perktold, Josef,                              Cimrman, Robert,                              Henriksen, Ian,                              Quintero, E. A.,                              Harris, Charles R.,                              Archibald, Anne M.,                              Ribeiro, Antônio H.,                              Pedregosa, Fabian,                              van Mulbregt, Paul                              
Published in Nature methods (01.03.2020)
                   
      
      
                                                  Published in Nature methods (01.03.2020)
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          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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          COBRApy: COnstraints-Based Reconstruction and Analysis for Python
                                      
                                            Ebrahim, Ali,                              Lerman, Joshua A,                              Palsson, Bernhard O,                              Hyduke, Daniel R                              
Published in BMC systems biology (08.08.2013)
                   
      
      
                                                  Published in BMC systems biology (08.08.2013)
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          PyImageJ: A library for integrating ImageJ and Python
                                      
                                            Rueden, Curtis T.,                              Hiner, Mark C.,                              Evans, Edward L.,                              Pinkert, Michael A.,                              Lucas, Alice M.,                              Carpenter, Anne E.,                              Cimini, Beth A.,                              Eliceiri, Kevin W.                              
Published in Nature methods (01.11.2022)
                   
      
      
                                                  Published in Nature methods (01.11.2022)
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          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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          Concordance of copy number abnormality detection using SNP arrays and Multiplex Ligation-dependent Probe Amplification (MLPA) in acute lymphoblastic leukaemia
                                      
                                            Bashton, Matthew,                              Hollis, Robin,                              Ryan, Sarra,                              Schwab, Claire J.,                              Moppett, John,                              Harrison, Christine J.,                              Moorman, Anthony V.,                              Enshaei, Amir                              
Published in Scientific reports (08.01.2020)
                   
      
      
                                                  Published in Scientific reports (08.01.2020)
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          PyRates—A Python framework for rate-based neural simulations
                                      
                                            Gast, Richard,                              Rose, Daniel,                              Salomon, Christoph,                              Möller, Harald E.,                              Weiskopf, Nikolaus,                              Knösche, Thomas R.                              
Published in PloS one (16.12.2019)
                   
      
      
                                                  Published in PloS one (16.12.2019)
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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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          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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