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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
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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Journal Article
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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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
Simulated annealing aided genetic algorithm for gene selection from microarray data
Marjit, Shyam, Bhattacharyya, Trinav, Chatterjee, Bitanu, Sarkar, Ram
Published in Computers in biology and medicine (01.05.2023)
Published in Computers in biology and medicine (01.05.2023)
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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
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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Journal Article
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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Journal Article
Combining high throughput array synthesis and growth algorithm to discover TNF-α binders with new structures and properties
Lin, Weilin, Gandhi, Shanil, Bhattarai, Prabesh, Kasa, Keida, Kizil, Caghan, Zhang, Yixin
Published in European journal of medicinal chemistry (15.02.2023)
Published in European journal of medicinal chemistry (15.02.2023)
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Journal Article