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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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Journal Article
Image processing for electron microscopy single-particle analysis using XMIPP
Scheres, Sjors H W, Núñez-Ramírez, Rafael, Sorzano, Carlos O S, Carazo, José María, Marabini, Roberto
Published in Nature protocols (01.06.2008)
Published in Nature protocols (01.06.2008)
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Journal Article
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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Journal Article
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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Journal Article
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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Journal Article
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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Journal Article
Tools and Algorithms for the Construction and Analysis of Systems: 27th International Conference, TACAS 2021, Held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2021, Luxembourg City, Luxembourg, March 27 – April 1, 2021, Proceedings, Part II
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ASV portal: an interface to DNA-based biodiversity data in the Living Atlas
Prager, Maria, Lundin, Daniel, Ronquist, Fredrik, Andersson, Anders F.
Published in BMC Bioinformatics (05.01.2023)
Published in BMC Bioinformatics (05.01.2023)
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Journal Article
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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Journal Article
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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