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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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          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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          Model of temperature, evaporation, and productivity in elevated experimental algae raceways and comparison with commercial raceways
                                      
                                            Khawam, George,                              Waller, Peter,                              Gao, Song,                              Edmundson, Scott,                              Wigmosta, Mark S.,                              Ogden, Kimberly                              
Published in Algal research (Amsterdam) (01.05.2019)
                   
      
      
                                                  Published in Algal research (Amsterdam) (01.05.2019)
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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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          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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          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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          Procrustes: A python library to find transformations that maximize the similarity between matrices
                                      
                                            Meng, Fanwang,                              Richer, Michael,                              Tehrani, Alireza,                              La, Jonathan,                              Kim, Taewon David,                              Ayers, Paul W.,                              Heidar-Zadeh, Farnaz                              
Published in Computer physics communications (01.07.2022)
                   
      
      
                                                  Published in Computer physics communications (01.07.2022)
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          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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