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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
Python workflow for the selection and identification of marker peptides—proof-of-principle study with heated milk
Kuhnen, Gesine, Class, Lisa-Carina, Badekow, Svenja, Hanisch, Kim Lara, Rohn, Sascha, Kuballa, Jürgen
Published in Analytical and bioanalytical chemistry (01.06.2024)
Published in Analytical and bioanalytical chemistry (01.06.2024)
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Journal Article
SAB: An open-access Python-based integrated platform for fully automated emergent sustainability assessment of biorefineries
Zarafshani, Hanie, Watjanatepin, Ponnapat, Navare, Kranti, Sauve, Giovanna, Van Acker, Karel
Published in The international journal of life cycle assessment (01.04.2024)
Published in The international journal of life cycle assessment (01.04.2024)
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Journal Article
Reproducible image-based profiling with Pycytominer
Serrano, Erik, Chandrasekaran, Srinivas Niranj, Bunten, Dave, Brewer, Kenneth I., Tomkinson, Jenna, Kern, Roshan, Bornholdt, Michael, Fleming, Stephen J., Pei, Ruifan, Arevalo, John, Tsang, Hillary, Rubinetti, Vincent, Tromans-Coia, Callum, Becker, Tim, Weisbart, Erin, Bunne, Charlotte, Kalinin, Alexandr A., Senft, Rebecca, Taylor, Stephen J., Jamali, Nasim, Adeboye, Adeniyi, Abbasi, Hamdah Shafqat, Goodman, Allen, Caicedo, Juan C., Carpenter, Anne E., Cimini, Beth A., Singh, Shantanu, Way, Gregory P.
Published in Nature methods (01.04.2025)
Published in Nature methods (01.04.2025)
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Journal Article
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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Journal Article
A computational framework for ptychographic reconstructions
Enders, B., Thibault, P.
Published in Proceedings of the Royal Society. A, Mathematical, physical, and engineering sciences (01.12.2016)
Published in Proceedings of the Royal Society. A, Mathematical, physical, and engineering sciences (01.12.2016)
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Journal Article
LASSIM—A network inference toolbox for genome-wide mechanistic modeling
Magnusson, Rasmus, Mariotti, Guido Pio, Köpsén, Mattias, Lövfors, William, Gawel, Danuta R., Jörnsten, Rebecka, Linde, Jörg, Nordling, Torbjörn E. M., Nyman, Elin, Schulze, Sylvie, Nestor, Colm E., Zhang, Huan, Cedersund, Gunnar, Benson, Mikael, Tjärnberg, Andreas, Gustafsson, Mika
Published in PLoS computational biology (01.06.2017)
Published in PLoS computational biology (01.06.2017)
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Journal Article
PyAGH: a python package to fast construct kinship matrices based on different levels of omic data
Zhao, Wei, Qadri, Qamar Raza, Zhang, Zhenyang, Wang, Zhen, Pan, Yuchun, Wang, Qishan, Zhang, Zhe
Published in BMC bioinformatics (18.04.2023)
Published in BMC bioinformatics (18.04.2023)
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Journal Article