Search Results - (( (statneneeeneeneeline OR stateed) python code analysis ) OR ( state python code analysis ))*

Analysis methods and code for very high-precision mass measurements of unstable isotopes by Karthein, J., Atanasov, D., Blaum, K., Lunney, D., Manea, V., Mougeot, M.

“…We present a robust analysis code developed in the Python language and incorporating libraries of the ROOT data analysis framework for the state-of-the-art mass spectrometry method called phase…”
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libRoadRunner 2.0: a high performance SBML simulation and analysis library by Welsh, Ciaran, Xu, Jin, Smith, Lucian, König, Matthias, Choi, Kiri, Sauro, Herbert M

“…Abstract Motivation This article presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using the systems biology markup language (SBML…”
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GSEApy: a comprehensive package for performing gene set enrichment analysis in Python by Fang, Zhuoqing, Liu, Xinyuan, Peltz, Gary

“…Abstract Motivation Gene set enrichment analysis (GSEA) is a commonly used algorithm for characterizing gene expression changes…”
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GPT-4.1 Sets the Standard in Automated Experiment Design Using Novel Python Libraries by Fachada, Nuno, Fernandes, Daniel, Fernandes, Carlos M., Ferreira-Saraiva, Bruno D., Matos-Carvalho, João P.

“… unfamiliar Python APIs for complex computational experiments remains poorly characterized. This study systematically benchmarks a selection of state-of-the-art LLMs in generating functional Python code for two increasingly challenging scenarios…”
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VULCAN: An Open-source, Validated Chemical Kinetics Python Code for Exoplanetary Atmospheres by Tsai, Shang-Min, Lyons, James R., Grosheintz, Luc, Rimmer, Paul B., Kitzmann, Daniel, Heng, Kevin

“…We present an open-source and validated chemical kinetics code for studying hot exoplanetary atmospheres, which we name VULCAN…”
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MechElastic: A Python library for analysis of mechanical and elastic properties of bulk and 2D materials by Singh, Sobhit, Lang, Logan, Dovale-Farelo, Viviana, Herath, Uthpala, Tavadze, Pedram, Coudert, François-Xavier, Romero, Aldo H.

“…The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix (Cij…”
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scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data by Faure, Louis, Soldatov, Ruslan, Kharchenko, Peter V, Adameyko, Igor

“…Abstract Summary scFates provides an extensive toolset for the analysis of dynamic trajectories comprising tree learning, feature association testing, branch differential expression and with a…”
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pyIAST: Ideal adsorbed solution theory (IAST) Python package by Simon, Cory M., Smit, Berend, Haranczyk, Maciej

“… We present an open-source, user-friendly Python package, pyIAST, to perform IAST calculations for an arbitrary number of components…”
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PHOTONAI—A Python API for rapid machine learning model development by Leenings, Ramona, Winter, Nils Ralf, Plagwitz, Lucas, Holstein, Vincent, Ernsting, Jan, Sarink, Kelvin, Fisch, Lukas, Steenweg, Jakob, Kleine-Vennekate, Leon, Gebker, Julian, Emden, Daniel, Grotegerd, Dominik, Opel, Nils, Risse, Benjamin, Jiang, Xiaoyi, Dannlowski, Udo, Hahn, Tim

“…PHOTONAI is a high-level Python API designed to simplify and accelerate machine learning model development…”
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pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods by Behdenna, Abdelkader, Colange, Maximilien, Haziza, Julien, Gema, Aryo, Appé, Guillaume, Azencott, Chloé-Agathe, Nordor, Akpéli

“… Results In this technical note, we present a new Python implementation of ComBat and ComBat-Seq…”
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stk: A python toolkit for supramolecular assembly by Turcani, Lukas, Berardo, Enrico, Jelfs, Kim E.

“… stk is a modular, extensible and open‐source Python library that provides a simple Python API and integration with third party computational codes…”
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SciPy 1.0: fundamental algorithms for scientific computing in Python by 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

“… Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages…”
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PyNoetic: A modular python framework for no-code development of EEG brain-computer interfaces by Singh, Gursimran, Chharia, Aviral, Upadhyay, Rahul, Kumar, Vinay, Longo, Luca

“… PyNoetic is one of the very few frameworks in Python that encompasses the entire BCI design pipeline, from stimulus presentation and data…”
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Snakes on a Spaceship - An Overview of Python in Heliophysics by Burrell, A.G., Halford, A., Klenzing, J., Stoneback, R. A., Morley, S. K., Annex, A. M., Laundal, K. M., Kellerman, A. C., Stansby, D., Ma, J.

“…Computational analysis has become ubiquitous within the heliophysics community. However, community standards for peer review of codes and analysis have lagged behind these developments…”
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GPAW: An open Python package for electronic structure calculations by Mortensen, Jens Jørgen, Larsen, Ask Hjorth, Kuisma, Mikael, Ivanov, Aleksei V, Taghizadeh, Alireza, Peterson, Andrew, Haldar, Anubhab, Dohn, Asmus Ougaard, Schäfer, Christian, Jónsson, Elvar Örn, Hermes, Eric D, Nilsson, Fredrik Andreas, Kastlunger, Georg, Levi, Gianluca, Jónsson, Hannes, Häkkinen, Hannu, Fojt, Jakub, Kangsabanik, Jiban, Sødequist, Joachim, Lehtomäki, Jouko, Heske, Julian, Enkovaara, Jussi, Winther, Kirsten Trøstrup, Dulak, Marcin, Melander, Marko M, Ovesen, Martin, Louhivuori, Martti, Walter, Michael, Gjerding, Morten, Lopez-Acevedo, Olga, Erhart, Paul, Warmbier, Robert, Würdemann, Rolf, Kaappa, Sami, Latini, Simone, Boland, Tara Maria, Bligaard, Thomas, Skovhus, Thorbjørn, Susi, Toma, Maxson, Tristan, Rossi, Tuomas, Chen, Xi, Schmerwitz, Yorick Leonard A, Schiøtz, Jakob, Olsen, Thomas, Jacobsen, Karsten Wedel, Thygesen, Kristian Sommer

“…We review the GPAW open-source Python package for electronic structure calculations…”
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Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier by Kim, Eiru, Hart, Traver

“… We previously described the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm for accurate classification of gene essentiality from short hairpin RNA and CRISPR/Cas9 genome-wide genetic screens…”
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Python code smells detection using conventional machine learning models by Sandouka, Rana, Aljamaan, Hamoud

“… This article proposes a Python code smell dataset for Large Class and Long Method code smells…”
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CRYSTALpytools: A Python infrastructure for the Crystal code by Camino, Bruno, Zhou, Huanyu, Ascrizzi, Eleonora, Boccuni, Alberto, Bodo, Filippo, Cossard, Alessandro, Mitoli, Davide, Ferrari, Anna Maria, Erba, Alessandro, Harrison, Nicholas M.

“…CRYSTALpytools is an open source Python project available on GitHub that implements a user-friendly interface to the Crystal code for quantum-mechanical condensed matter simulations…”
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Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals by Combrisson, Etienne, Nest, Timothy, Brovelli, Andrea, Ince, Robin A. A., Soto, Juan L. P., Guillot, Aymeric, Jerbi, Karim

“… Current research in the field is not only hampered by the absence of a gold standard for PAC analysis, but also by the computational costs of running exhaustive computations on large and high…”
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galpy: A python LIBRARY FOR GALACTIC DYNAMICS by Bovy, Jo

“…I describe the design, implementation, and usage of galpy, a python package for galactic-dynamics calculations…”
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