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SciPy 1.0: fundamental algorithms for scientific computing in Python
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
Published in Nature methods (01.03.2020)
Published in Nature methods (01.03.2020)
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Journal Article
PHOTONAI—A Python API for rapid machine learning model development
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
Published in PloS one (21.07.2021)
Published in PloS one (21.07.2021)
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Journal Article
PyNoetic: A modular python framework for no-code development of EEG brain-computer interfaces
Singh, Gursimran, Chharia, Aviral, Upadhyay, Rahul, Kumar, Vinay, Longo, Luca
Published in PloS one (06.08.2025)
Published in PloS one (06.08.2025)
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Journal Article
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
Ebrahim, Ali, Lerman, Joshua A, Palsson, Bernhard O, Hyduke, Daniel R
Published in BMC systems biology (08.08.2013)
Published in BMC systems biology (08.08.2013)
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Journal Article
SPOTting Model Parameters Using a Ready-Made Python Package
Houska, Tobias, Kraft, Philipp, Chamorro-Chavez, Alejandro, Breuer, Lutz
Published in PloS one (17.12.2015)
Published in PloS one (17.12.2015)
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Journal Article
pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment
Warris, Sven, Timal, N. Roshan N., Kempenaar, Marcel, Poortinga, Arne M., van de Geest, Henri, Varbanescu, Ana L., Nap, Jan-Peter
Published in PloS one (02.01.2018)
Published in PloS one (02.01.2018)
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Journal Article
Empowering ecological modellers with a PERFICT workflow: Seamlessly linking data, parameterisation, prediction, validation and visualisation
Barros, Ceres, Luo, Yong, Chubaty, Alex M., Eddy, Ian M. S., Micheletti, Tatiane, Boisvenue, Céline, Andison, David W., Cumming, Steven G., McIntire, Eliot J. B.
Published in Methods in ecology and evolution (01.01.2023)
Published in Methods in ecology and evolution (01.01.2023)
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Journal Article
BioCoder: a benchmark for bioinformatics code generation with large language models
Tang, Xiangru, Qian, Bill, Gao, Rick, Chen, Jiakang, Chen, Xinyun, Gerstein, Mark B
Published in Bioinformatics (Oxford, England) (28.06.2024)
Published in Bioinformatics (Oxford, England) (28.06.2024)
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Journal Article
Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing
Duez, Marc, Giraud, Mathieu, Herbert, Ryan, Rocher, Tatiana, Salson, Mikaël, Thonier, Florian
Published in PloS one (11.11.2016)
Published in PloS one (11.11.2016)
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Journal Article
FeAture Explorer (FAE): A tool for developing and comparing radiomics models
Song, Yang, Zhang, Jing, Zhang, Yu-dong, Hou, Ying, Yan, Xu, Wang, Yida, Zhou, Minxiong, Yao, Ye-feng, Yang, Guang
Published in PloS one (17.08.2020)
Published in PloS one (17.08.2020)
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Journal Article
Segmentation, tracking and cell cycle analysis of live-cell imaging data with Cell-ACDC
Padovani, Francesco, Mairhörmann, Benedikt, Falter-Braun, Pascal, Lengefeld, Jette, Schmoller, Kurt M.
Published in BMC biology (05.08.2022)
Published in BMC biology (05.08.2022)
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Journal Article