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Python Data Analyst's Toolkit - Learn Python and Python-Based Libraries with Applications in Data Analysis and Statistics by Rajagopalan, Gayathri

“… The code is presented in Jupyter notebooks that can further be adapted and extended. This book is divided into three parts - programming with Python, data analysis and visualization, and statistics…”
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PyLAT: Python LAMMPS Analysis Tools by Humbert, Michael T, Zhang, Yong, Maginn, Edward J

“… Here we describe a suite of open-source Python-based postprocessing routines we have developed called PyLAT…”
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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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Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics by Goloborodko, Anton A., Levitsky, Lev I., Ivanov, Mark V., Gorshkov, Mikhail V.

“…Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics…”
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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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Assessing code readability in Python programming courses using eye‐tracking by Segedinac, Milan, Savić, Goran, Zeljković, Ivana, Slivka, Jelena, Konjović, Zora

“… This paper assesses the readability of Python code statements commonly used in undergraduate programming courses…”
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Detecting Memory Errors in Python Native Code by Tracking Object Lifecycle with Reference Count by Ma, Xutong, Yan, Jiwei, Zhang, Hao, Yan, Jun, Zhang, Jian

“… To detect such problems, state-of-the-art approaches have made groundbreaking contributions to identifying inappropriate final refcount values before returning from native code to Python…”
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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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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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The fast azimuthal integration Python library: pyFAI by Ashiotis, Giannis, Deschildre, Aurore, Nawaz, Zubair, Wright, Jonathan P., Karkoulis, Dimitrios, Picca, Frédéric Emmanuel, Kieffer, Jérôme

“… It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline…”
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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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Mitigating the Uncertainty and Imprecision of Log-Based Code Coverage Without Requiring Additional Logging Statements by Xu, Xiaoyan, Cogo, Filipe R., McIntosh, Shane

“…Understanding code coverage is an important precursor to software maintenance activities (e.g., better testing…”
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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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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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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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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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DQC: A Python program package for differentiable quantum chemistry by Kasim, Muhammad F, Lehtola, Susi, Vinko, Sam M

“… Here, we present an open-source differentiable quantum chemistry simulation code and explore applications facilitated by automatic differentiation: (1) calculating molecular perturbation properties, (2) reoptimizing a basis set for hydrocarbons, (3) checking the stability of self-consistent field wave functions, and (4) predicting molecular properties via alchemical perturbations…”
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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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