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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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          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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          MetPy: A Meteorological Python Library for Data Analysis and Visualization
                                      
                                            May, Ryan M.,                              Goebbert, Kevin H.,                              Thielen, Jonathan E.,                              Leeman, John R.,                              Camron, M. Drew,                              Bruick, Zachary,                              Bruning, Eric C.,                              Manser, Russell P.,                              Arms, Sean C.,                              Marsh, Patrick T.                              
Published in Bulletin of the American Meteorological Society (01.10.2022)
                   
      
      
                                                  Published in Bulletin of the American Meteorological Society (01.10.2022)
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          Parallel distributed computing using Python
                                      
                                            Dalcin, Lisandro D.,                              Paz, Rodrigo R.,                              Kler, Pablo A.,                              Cosimo, Alejandro                              
Published in Advances in water resources (01.09.2011)
                   
      
      
                                                  Published in Advances in water resources (01.09.2011)
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          Core Imaging Library - Part I: a versatile Python framework for tomographic imaging
                                      
                                            Jørgensen, J. S.,                              Ametova, E.,                              Burca, G.,                              Fardell, G.,                              Papoutsellis, E.,                              Pasca, E.,                              Thielemans, K.,                              Turner, M.,                              Warr, R.,                              Lionheart, W. R. B.,                              Withers, P. J.                              
Published in Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences (23.08.2021)
                   
      
      
                                                  Published in Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences (23.08.2021)
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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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          AnalyZr: A Python application for zircon grain image segmentation and shape analysis
                                      
                                            Scharf, T.,                              Kirkland, C.L.,                              Daggitt, M.L.,                              Barham, M.,                              Puzyrev, V.                              
Published in Computers & geosciences (01.05.2022)
                   
      
      
                                                  Published in Computers & geosciences (01.05.2022)
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          Author Correction: 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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          An accessible, efficient, and accurate natural language processing method for extracting diagnostic data from pathology reports
                                      
                                            Lam, Hansen,                              Nguyen, Freddy,                              Wang, Xintong,                              Stock, Aryeh,                              Lenskaya, Volha,                              Kooshesh, Maryam,                              Li, Peizi,                              Qazi, Mohammad,                              Wang, Shenyu,                              Dehghan, Mitra,                              Qian, Xia,                              Si, Qiusheng,                              Polydorides, Alexandros D.                              
Published in Journal of pathology informatics (01.01.2022)
                   
      
      
                                                  Published in Journal of pathology informatics (01.01.2022)
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