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Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS

by Johnson, Jeanette A. I., Tsang, Ashley P., Mitchell, Jacob T., Zhou, David L., Bowden, Julia, Davis-Marcisak, Emily, Sherman, Thomas, Liefeld, Ted, Loth, Melanie, Goff, Loyal A., Zimmerman, Jacquelyn W., Kinny-Köster, Ben, Jaffee, Elizabeth M., Tamayo, Pablo, Mesirov, Jill P., Reich, Michael, Fertig, Elana J., Stein-O’Brien, Genevieve L.
Published in Nature protocols (01.12.2023)

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MEG and EEG data analysis with MNE-Python

by Gramfort, Alexandre
Published in Frontiers in neuroscience (26.12.2013)

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PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data

by Georgi, Benjamin, Costa, Ivan Gesteira, Schliep, Alexander
Published in BMC bioinformatics (06.01.2010)

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Python for chemistry : an introduction to python algorithms, simulations, and programing for chemistry

by Kanagasabapathy, M.
Year of Publication 2023

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eBook Book

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Machine Learning Guide for Oil and Gas Using Python - A Step-by-Step Breakdown with Data, Algorithms, Codes, and Applications

by Belyadi, Hoss, Haghighat, Alireza
Year of Publication 2021

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eBook

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Design of Heuristic Algorithms for Hard Optimization: With Python Codes for the Travelling Salesman Problem

by Taillard, Eric D
Year of Publication 2023

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eBook Publication

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Nmrglue: an open source Python package for the analysis of multidimensional NMR data

by Helmus, Jonathan J., Jaroniec, Christopher P.
Published in Journal of biomolecular NMR (01.04.2013)

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Prediction of stunting and its socioeconomic determinants among adolescent girls in Ethiopia using machine learning algorithms

by Zemariam, Alemu Birara, Abate, Biruk Beletew, Alamaw, Addis Wondmagegn, Lake, Eyob shitie, Yilak, Gizachew, Ayele, Mulat, Tilahun, Befkad Derese, Ngusie, Habtamu Setegn
Published in PloS one (24.01.2025)

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Python tools for structural tasks in chemistry

by Ryzhkov, Fedor V., Ryzhkova, Yuliya E., Elinson, Michail N.
Published in Molecular diversity (01.08.2025)

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PyImageJ: A library for integrating ImageJ and Python

by Rueden, Curtis T., Hiner, Mark C., Evans, Edward L., Pinkert, Michael A., Lucas, Alice M., Carpenter, Anne E., Cimini, Beth A., Eliceiri, Kevin W.
Published in Nature methods (01.11.2022)

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pyMPSLib: A robust and scalable open-source Python library for mutiple-point statistical simulation

by Chen, Qiyu, Zhou, Ruihong, Liu, Cui, Huang, Qianhong, Cui, Zhesi, Liu, Gang
Published in Earth science informatics (01.12.2023)

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PyRates—A Python framework for rate-based neural simulations

by Gast, Richard, Rose, Daniel, Salomon, Christoph, Möller, Harald E., Weiskopf, Nikolaus, Knösche, Thomas R.
Published in PloS one (16.12.2019)

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Music Representation and Transformation in Software: Structure and Algorithms in Python

by Pazel, Donald P
Year of Publication 2022

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eBook

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Data Science Toolkit: An all-in-one python library to help researchers and practitioners in implementing data science-related algorithms with less effort

by El Hachimi, Chouaib, Belaqziz, Salwa, Khabba, Saïd, Chehbouni, Abdelghani
Published in Software impacts (01.05.2022)

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Towards understanding bugs in Python interpreters

by Liu, Di, Feng, Yang, Yan, Yanyan, Xu, Baowen
Published in Empirical software engineering : an international journal (01.01.2023)

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SAB: An open-access Python-based integrated platform for fully automated emergent sustainability assessment of biorefineries

by Zarafshani, Hanie, Watjanatepin, Ponnapat, Navare, Kranti, Sauve, Giovanna, Van Acker, Karel
Published in The international journal of life cycle assessment (01.04.2024)

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A new general method for assigning frequencies with low spillover through structural modifications

by Liu, Zihao, Pang, Jichao, Ouyang, Huajiang, Xie, Guocheng
Published in Journal of low frequency noise, vibration, and active control (01.12.2023)

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SciKit Digital Health: Python Package for Streamlined Wearable Inertial Sensor Data Processing

by Adamowicz, Lukas, Christakis, Yiorgos, Czech, Matthew D, Adamusiak, Tomasz
Published in JMIR mHealth and uHealth (21.04.2022)

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gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support

by Irrgang, M. Eric, Davis, Caroline, Kasson, Peter M.
Published in PLoS computational biology (01.02.2022)

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VMseg: Using spatial variance to automatically segment retinal non-perfusion on OCT-angiography

by LE BOITE, Hugo, COUTURIER, Aude, TADAYONI, Ramin, LAMARD, Mathieu, QUELLEC, Gwenolé
Published in PloS one (07.08.2024)

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