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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 by 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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Introduction to computational causal inference using reproducible Stata, R, and Python code: A tutorial by 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 by 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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A python framework for multi-agent simulation of networked resource systems by Knox, Stephen, Meier, Philipp, Yoon, Jim, Harou, Julien J.

“… This common interface acts as an agreed mode of communication for all contributors. We propose the Python Network Simulation (Pynsim…”
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Percolation theory using Python by 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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MagPySV: A Python Package for Processing and Denoising Geomagnetic Observatory Data by Cox, G. A., Brown, W. J., Billingham, L., Holme, R.

“…). However, current data processing methods rely on piecemeal closed‐source codes or are performed on an ad hoc basis, hampering efforts to reproduce data sets underlying published results…”
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Superposed epoch analysis using time-normalization: A Python tool for statistical event analysis by Walton, Samuel D., Murphy, Kyle R.

“…A superposed epoch analysis (SEA) is a simple, yet powerful statistical analysis technique, used to identify patterns in the temporal evolution of observed quantities relative to defined epochs…”
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Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data by Pakkir Shah, Abzer K., Walter, Axel, Ottosson, Filip, Russo, Francesco, Navarro-Diaz, Marcelo, Boldt, Judith, Kalinski, Jarmo-Charles J., Kontou, Eftychia Eva, Elofson, James, Polyzois, Alexandros, González-Marín, Carolina, Farrell, Shane, Aggerbeck, Marie R., Pruksatrakul, Thapanee, Chan, Nathan, Wang, Yunshu, Pöchhacker, Magdalena, Brungs, Corinna, Cámara, Beatriz, Caraballo-Rodríguez, Andrés Mauricio, Cumsille, Andres, de Oliveira, Fernanda, Dührkop, Kai, El Abiead, Yasin, Geibel, Christian, Graves, Lana G., Hansen, Martin, Heuckeroth, Steffen, Knoblauch, Simon, Kostenko, Anastasiia, Kuijpers, Mirte C. M., Mildau, Kevin, Papadopoulos Lambidis, Stilianos, Portal Gomes, Paulo Wender, Schramm, Tilman, Steuer-Lodd, Karoline, Stincone, Paolo, Tayyab, Sibgha, Vitale, Giovanni Andrea, Wagner, Berenike C., Xing, Shipei, Yazzie, Marquis T., Zuffa, Simone, de Kruijff, Martinus, Beemelmanns, Christine, Link, Hannes, Mayer, Christoph, van der Hooft, Justin J. J., Damiani, Tito, Pluskal, Tomáš, Dorrestein, Pieter, Stanstrup, Jan, Schmid, Robin, Wang, Mingxun, Aron, Allegra, Ernst, Madeleine, Petras, Daniel

“… We provide explanations and code in two scripting languages (R and Python) as well…”
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Applications of Python in Solving Physical Chemistry Problems by Singh, Jyoti, Passey, Sarita, Basu, Debasmi, Katyal, Tushar, Verma, Hemant

“…This article, presented in two parts, aims to serve as an introduction to the fundamentals of Python programming and data analysis in the context of physical chemistry experiments. In this part (Part…”
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Confidence of a k-Nearest Neighbors Python Algorithm for the 3D Visualization of Sedimentary Porous Media by Martín-Martín, Manuel, Evolución Geodinámica de la Cordillera Bética Oriental y de la Plataforma Marina de Alicante, Cabezas, David, Alcalá, Francisco J, Universidad de Alicante. Departamento de Ciencias de la Tierra y del Medio Ambiente, Bullejos, Manuel

“…Research Project PID2020-114381GB-100 of the Spanish Ministry of Science and Innovation, Research Project 101086497 of the Horizon Europe Framework Programme…”
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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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Unmixing of Magnetic Hysteresis Loops Through a Modified Gamma‐Cauchy Exponential Model by Bellon, U. D., Trindade, R. I. F., Williams, W.

“…Quantifying the contributions of distinct mineral populations in bulk magnetic experiments greatly enhances the analysis of environmental and rock magnetism studies…”
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bmotif: A package for motif analyses of bipartite networks by Simmons, Benno I., Sweering, Michelle J. M., Schillinger, Maybritt, Dicks, Lynn V., Sutherland, William J., Di Clemente, Riccardo, Matthiopoulos, Jason

“…Bipartite networks are widely used to represent a diverse range of species interactions, such as pollination, herbivory, parasitism and seed dispersal. The…”
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Nestedness for Dummies (NeD): A user friendly web interface for exploratory nestedness analysis by Strona, Giovanni, Galli, Paolo, Seveso, Davide, Montano, Simone, Fattorini, Simone

“…Recent theoretical advances in nestedness analysis have led to the introduction of several alternative metrics to overcome most of the problems biasing the use of matrix 'temperature' calculated…”
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Statistics Using Python by 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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Applications of Python in Solving Physical Chemistry Problems: Part 1 by Singh, Jyoti, Passey, Sarita, Basu, Debasmi, Katyal, Tushar, Verma, Hemant

“…This article, presented in two parts, aims to serve as an introduction to the fundamentals of Python programming and data analysis in the context of physical chemistry experiments. In this part (Part…”
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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 by 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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fenics_ice 1.0: a framework for quantifying initialization uncertainty for time-dependent ice sheet models by Koziol, Conrad P., Todd, Joe A., Goldberg, Daniel N., Maddison, James R.

“… Numerical codes simulating the evolution of ice sheets can potentially quantify this future contribution…”
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Statistical Analyses and Reproducible Research by Gentleman, Robert, Temple Lang, Duncan

“…It is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, and so on with the documents that describe and rely…”
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Dashboard Design to Analyze Chemical Weathering of Clastic Sediments by Babu, Vinay, Bhan, Uday, Devaraju, J., Rai, Santosh K.

“…For a provenance study and characterization of different types of sedimentological processes that affect weathering, information on chemical weathering of…”
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