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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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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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powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions by Alstott, Jeff, Bullmore, Ed, Plenz, Dietmar

“… In order to greatly decrease the barriers to using good statistical methods for fitting power law distributions, we developed the powerlaw Python package…”
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Pytim: A python package for the interfacial analysis of molecular simulations by Sega, Marcello, Hantal, György, Fábián, Balázs, Jedlovszky, Pál

“…Pytim is a versatile python framework for the analysis of interfacial properties in molecular simulations…”
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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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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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COBRApy: COnstraints-Based Reconstruction and Analysis for Python by Ebrahim, Ali, Lerman, Joshua A, Palsson, Bernhard O, Hyduke, Daniel R

“…Background COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes…”
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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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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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Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique by Yang, Hang, Lu, Xiaoxin, Chang, Jiaxing, Chang, Qing, Zheng, Wen, Chen, Zehua, Yi, Huiguang

“… These limitations collectively impede the overall convenience and efficiency of the analysis. In this study, we introduce Kssdtree, an interactive Python package designed to address these challenges…”
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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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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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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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BatAnalysis: A Comprehensive Python Pipeline for Swift BAT Survey Analysis by Parsotan, Tyler, Laha, Sibasish, Palmer, David M., Lien, Amy, Cenko, S. Bradley, Krimm, Hans, Markwardt, Craig

“…The Swift Burst Alert Telescope (BAT) is a coded aperture gamma-ray instrument with a large field of view that primarily operates in survey mode when it is not…”
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OTSun, a python package for the optical analysis of solar-thermal collectors and photovoltaic cells with arbitrary geometry by Cardona, Gabriel, Pujol-Nadal, Ramon

“… We present here the open source python package OTSun, which applies the Fresnel equations in their most general form, without further simplifications, and is suitable for the simulation of both solar…”
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Cardio PyMEA: A user-friendly, open-source Python application for cardiomyocyte microelectrode array analysis by Dunham, Christopher S., Mackenzie, Madelynn E., Nakano, Haruko, Kim, Alexis R., Nakano, Atsushi, Stieg, Adam Z., Gimzewski, James K.

“…Open source analytical software for the analysis of electrophysiological cardiomyocyte data offers a variety of new functionalities to complement closed-source, proprietary tools…”
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CellProfiler plugins – An easy image analysis platform integration for containers and Python tools by Weisbart, Erin, Tromans‐Coia, Callum, Diaz‐Rohrer, Barbara, Stirling, David R., Garcia‐Fossa, Fernanda, Senft, Rebecca A., Hiner, Mark C., de Jesus, Marcelo B., Eliceiri, Kevin W., Cimini, Beth A.

“…CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code…”
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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

“…We review the GPAW open-source Python package for electronic structure calculations…”
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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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