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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
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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Journal Article
Domain Knowledge Matters: Improving Prompts with Fix Templates for Repairing Python Type Errors
Peng, Yun, Gao, Shuzheng, Gao, Cuiyun, Huo, Yintong, Lyu, Michael R.
Published in Proceedings / International Conference on Software Engineering (14.04.2024)
Published in Proceedings / International Conference on Software Engineering (14.04.2024)
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Conference Proceeding
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
Towards understanding bugs in Python interpreters
Liu, Di, Feng, Yang, Yan, Yanyan, Xu, Baowen
Published in Empirical software engineering : an international journal (01.01.2023)
Published in Empirical software engineering : an international journal (01.01.2023)
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Journal Article
PyRates—A Python framework for rate-based neural simulations
Gast, Richard, Rose, Daniel, Salomon, Christoph, Möller, Harald E., Weiskopf, Nikolaus, Knösche, Thomas R.
Published in PloS one (16.12.2019)
Published in PloS one (16.12.2019)
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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
Morphoscanner2.0: A new python module for analysis of molecular dynamics simulations
Fontana, Federico, Carlino, Calogero, Malik, Ashish, Gelain, Fabrizio
Published in PloS one (27.04.2023)
Published in PloS one (27.04.2023)
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Journal Article
Interest objects detection for self-driving cars using a Deep learning approach
Awandu, Chibundu, Lamichhane, Santosh, Tyson, Shaquan, Kalenga, Aldridge, Mwase, Buchizya, Brown, Tianna, Calderon, Juan
Published in Florida scientist (01.09.2024)
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Published in Florida scientist (01.09.2024)
Journal Article
pyMPSLib: A robust and scalable open-source Python library for mutiple-point statistical simulation
Chen, Qiyu, Zhou, Ruihong, Liu, Cui, Huang, Qianhong, Cui, Zhesi, Liu, Gang
Published in Earth science informatics (01.12.2023)
Published in Earth science informatics (01.12.2023)
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Journal Article
SciKit Digital Health: Python Package for Streamlined Wearable Inertial Sensor Data Processing
Adamowicz, Lukas, Christakis, Yiorgos, Czech, Matthew D, Adamusiak, Tomasz
Published in JMIR mHealth and uHealth (21.04.2022)
Published in JMIR mHealth and uHealth (21.04.2022)
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Journal Article
Comparative Analysis of AI Models for Python Code Generation: A HumanEval Benchmark Study
Bayram, Ali, Menekse Dalveren, Gonca Gokce, Derawi, Mohammad
Published in Applied sciences (10.09.2025)
Published in Applied sciences (10.09.2025)
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Journal Article
ABC-SysBio—approximate Bayesian computation in Python with GPU support
Liepe, Juliane, Barnes, Chris, Cule, Erika, Erguler, Kamil, Kirk, Paul, Toni, Tina, Stumpf, Michael P.H.
Published in Bioinformatics (15.07.2010)
Published in Bioinformatics (15.07.2010)
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Journal Article
GLAMbox: A Python toolbox for investigating the association between gaze allocation and decision behaviour
Molter, Felix, Thomas, Armin W, Heekeren, Hauke R, Mohr, Peter N. C
Published in PloS one (16.12.2019)
Published in PloS one (16.12.2019)
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Journal Article
Evaluating machine learning algorithms to predict lameness in dairy cattle
Neupane, Rajesh, Aryal, Ashrant, Haeussermann, Angelika, Hartung, Eberhard, Pinedo, Pablo, Paudyal, Sushil
Published in PloS one (18.07.2024)
Published in PloS one (18.07.2024)
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Journal Article
PODPAC: open-source Python software for enabling harmonized, plug-and-play processing of disparate earth observation data sets and seamless transition onto the serverless cloud by earth scientists
Ueckermann, Mattheus P., Bieszczad, Jerry, Entekhabi, Dara, Shapiro, Marc L., Callendar, David R., Sullivan, David, Milloy, Jeffrey
Published in Earth science informatics (01.12.2020)
Published in Earth science informatics (01.12.2020)
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Journal Article
A novel fractal interpolation function algorithm for fractal dimension estimation and coastline geometry reconstruction: a case study of the coastline of Kingdom of Saudi Arabia
Husain, Akhlaq, Gumma, Suhas, Sajid, Mohammad, Reddy, Jaideep, Alresheedi, Mohammad T.
Published in The European physical journal. B, Condensed matter physics (01.04.2024)
Published in The European physical journal. B, Condensed matter physics (01.04.2024)
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Journal Article