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Percolation theory using Python Autor Malthe-Sørenssen, Anders

“… Readers will learn how to generate, analyze, and comprehend data and models, with detailed theoretical discussions complemented by accessible computer codes…”
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Decoding the JAK-STAT Axis in Colorectal Cancer with AI-HOPE-JAK-STAT: A Conversational Artificial Intelligence Approach to Clinical–Genomic Integration Autor Yang, Ei-Wen, Waldrup, Brigette, Velazquez-Villarreal, Enrique

“…: AI-HOPE-JAK-STAT combines large language models (LLMs), a natural language-to-code engine, and harmonized public CRC datasets from cBioPortal…”
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Statistics Using Python Autor Campesato, Oswald

“…This book is designed to offer a fast-paced yet thorough introduction to essential statistical concepts using Python code samples, and aims to assist data scientists in their daily endeavors…”
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Introduction to computational causal inference using reproducible Stata, R, and Python code: A tutorial Autor Smith, Matthew J., Mansournia, Mohammad A., Maringe, Camille, Zivich, Paul N., Cole, Stephen R., Leyrat, Clémence, Belot, Aurélien, Rachet, Bernard, Luque‐Fernandez, Miguel A.

“…The main purpose of many medical studies is to estimate the effects of a treatment or exposure on an outcome. However, it is not always possible to randomize…”
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LiPydomics: A Python Package for Comprehensive Prediction of Lipid Collision Cross Sections and Retention Times and Analysis of Ion Mobility-Mass Spectrometry-Based Lipidomics Data Autor Ross, Dylan H, Cho, Jang Ho, Zhang, Rutan, Hines, Kelly M, Xu, Libin

“… Existing solutions for these data analysis challenges (i.e., multivariate statistics and lipid identification…”
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PyLAT: Python LAMMPS Analysis Tools Autor 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 Autor 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 Autor 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 Autor 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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From code to reliability: Python-powered Paraconsistent Logic for alarm detection in the power gris/ Do codigo a confiabilidade: Logica Paraconsistente impulsionada por Python para a deteccao de alarmes na rede de energia Autor de Oliveira, Joseffe Barroso, Gino, Joao Vitor Santa Rosa, de Lima, Carlos Jose, Filho, Joao Inacio da Silva

“… This application enables the comparison of triggered alarms with the resultant logical states obtained during the analysis…”
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stk: A python toolkit for supramolecular assembly Autor 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 Autor 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 Autor 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 Autor 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 Autor 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 Autor 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 Autor 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 Autor 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 Autor 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 Autor 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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