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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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          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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          Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN
                                      
                                            Kinman, Laurel F.,                              Powell, Barrett M.,                              Zhong, Ellen D.,                              Berger, Bonnie,                              Davis, Joseph H.                              
Published in Nature protocols (01.02.2023)
                   
      
      
                                                  Published in Nature protocols (01.02.2023)
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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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          Toward a unified framework for interpreting machine-learning models in neuroimaging
                                      
                                            Kohoutová, Lada,                              Heo, Juyeon,                              Cha, Sungmin,                              Lee, Sungwoo,                              Moon, Taesup,                              Wager, Tor D.,                              Woo, Choong-Wan                              
Published in Nature protocols (01.04.2020)
                   
      
      
                                                  Published in Nature protocols (01.04.2020)
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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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          ITEP: An integrated toolkit for exploration of microbial pan-genomes
                                      
                                            Benedict, Matthew N,                              Henriksen, James R,                              Metcalf, William W,                              Whitaker, Rachel J,                              Price, Nathan D                              
Published in BMC genomics (03.01.2014)
                   
      
      
                                                  Published in BMC genomics (03.01.2014)
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