Search Results - (( (statne OR state) python code analysis ) OR ( (statene OR state:id) python code analysis ))

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks by Naldi, Aurélien, Hernandez, Céline, Levy, Nicolas, Stoll, Gautier, Monteiro, Pedro T., Chaouiya, Claudine, Helikar, Tomáš, Zinovyev, Andrei, Calzone, Laurence, Cohen-Boulakia, Sarah, Thieffry, Denis, Paulevé, Loïc

“… The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve…”
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Algorithm-Aided Design with Python: Analysis of Technological Competence of Subjects by Pontes, Thiago Bessa, Miranda, Guilhermina Lobato, Celani, Gabriela Caffarena

“… on the basis of the 4C-ID instructional design model. These results are a sociodemographic analysis, and the technological competence of these subjects…”
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Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry by Röst, Hannes L, Schmitt, Uwe, Aebersold, Ruedi, Malmström, Lars

“… the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis…”
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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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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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Scikit-Dimension: A Python Package for Intrinsic Dimension Estimation by Bac, Jonathan, Mirkes, Evgeny M., Gorban, Alexander N., Tyukin, Ivan, Zinovyev, Andrei

“…). A number of methods have been suggested for the purpose of estimating ID, but no standard package to easily apply them one by one or all at once has been implemented in Python…”
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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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Deep learning for the diagnosis of mesial temporal lobe epilepsy by Sakashita, Kyoya, Akiyama, Yukinori, Hirano, Tsukasa, Sasagawa, Ayaka, Arihara, Masayasu, Kuribara, Tomoyoshi, Ochi, Satoko, Enatsu, Rei, Mikami, Takeshi, Mikuni, Nobuhiro

“… In this study, we used an AI program to diagnose MTLE. The image sets were processed using a code written in Python 3.7.4…”
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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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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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