Search Results - (( (statement OR state) python code analysis ) OR ( (stated OR state:new) python code analysis ))

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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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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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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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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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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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

“… This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies…”
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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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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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AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis by Isamura, Bienfait K., Lobb, Kevin A.

“…Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention…”
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Functional Python Programming: Use a functional approach to write succinct, expressive, and efficient Python code by Lott, Steven F

“…Python isn’t all about object-oriented programming. Discover a valuable way of thinking about code design through a function-first approach…”
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Gnocis: An integrated system for interactive and reproducible analysis and modelling of cis-regulatory elements in Python 3 by Bredesen-Aa, Bjørn André, Rehmsmeier, Marc

“… methods for the genome-wide prediction of candidate CREs. We here present Gnocis, a Python package that streamlines the analysis and the modelling of CRE sequences…”
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Methods and Benchmark for Detecting Cryptographic API Misuses in Python by Frantz, Miles, Xiao, Ya, Pias, Tanmoy Sarkar, Meng, Na, Yao, Danfeng

“… The current static code analysis tools for Python are unable to scan the increasing complexity of the source code…”
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Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python by Kuehl, Malte, Wong, Milagros N, Wanner, Nicola, Bonn, Stefan, Puelles, Victor G

“… However, their output consists of transcript count estimates that are subject to multiple biases and cannot be readily used with existing differential gene expression analysis tools in Python…”
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PETAL: a Python tool for deep analysis of biological pathways by Sgroi, Giuseppe, Russo, Giulia, Pappalardo, Francesco

“… Here, we developed PETAL, a Python tool that automatically explores and detects the most relevant nodes within a KEGG pathway, scanning and performing an in-depth search…”
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SBML2HYB: a Python interface for SBML compatible hybrid modeling by Pinto, José, Costa, Rafael S, Alexandre, Leonardo, Ramos, João, Oliveira, Rui

“…Abstract Summary Here, we present sbml2hyb, an easy-to-use standalone Python tool that facilitates the conversion of existing mechanistic models of biological systems in Systems Biology Markup Language (SBML…”
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Nmrglue: an open source Python package for the analysis of multidimensional NMR data by Helmus, Jonathan J., Jaroniec, Christopher P.

“… When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number…”
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pyMBE: The Python-based molecule builder for ESPResSo by Beyer, David, Torres, Paola B, Pineda, Sebastian P, Narambuena, Claudio F, Grad, Jean-Noël, Košovan, Peter, Blanco, Pablo M

“…We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software application to design custom coarse-grained (CG…”
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