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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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          LibSBML: an API Library for SBML
                                      
                                            Bornstein, Benjamin J.,                              Keating, Sarah M.,                              Jouraku, Akiya,                              Hucka, Michael                              
Published in Bioinformatics (15.03.2008)
                   
      
      
                                                  Published in Bioinformatics (15.03.2008)
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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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          lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R
                                      
                                            Khleborodova, Asya,                              Gamboa-Tuz, Samuel D,                              Ramos, Marcel,                              Segata, Nicola,                              Waldron, Levi,                              Oh, Sehyun                              
Published in Bioinformatics (Oxford, England) (28.11.2024)
                   
      
      
                                                  Published in Bioinformatics (Oxford, England) (28.11.2024)
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          The Remote Sensing and GIS Software Library (RSGISLib)
                                      
                                            Bunting, Peter,                              Clewley, Daniel,                              Lucas, Richard M.,                              Gillingham, Sam                              
Published in Computers & geosciences (01.01.2014)
                   
      
      
                                                  Published in Computers & geosciences (01.01.2014)
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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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          Pyg4ometry: A Python library for the creation of Monte Carlo radiation transport physical geometries
                                      
                                            Walker, S.D.,                              Abramov, A.,                              Nevay, L.J.,                              Shields, W.,                              Boogert, S.T.                              
Published in Computer physics communications (01.03.2022)
                   
      
      
                                                  Published in Computer physics communications (01.03.2022)
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