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Second-generation PLINK: rising to the challenge of larger and richer datasets 由 Christopher Chang, Carson C. Chow, Laurent CAM Tellier, Shashaank Vattikuti, Shaun Purcell, James J. Lee

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DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets 由 Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer

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CaFE: a tool for binding affinity prediction using end-point free energy methods 由 Hui Liu, Tingjun Hou

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Clinical records anonymisation and text extraction (CRATE): an open-source software system 由 Rudolf N. Cardinal

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The €100 lab: A 3D-printable open-source platform for fluorescence microscopy, optogenetics, and accurate temperature control during behaviour of zebrafish, Drosophila, and Caenorh... 由 André Maia Chagas, Lucia L. Prieto-Godino, Aristides B. Arrenberg, Tom Baden

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Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes 由 Steven Weaver, Stephen D. Shank, Stephanie J. Spielman, Michael Li, Spencer V. Muse, Sergei L. Kosakovsky Pond

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Implementation and applications of EMOD, an individual-based multi-disease modeling platform 由 Anna Bershteyn, Jaline Gerardin, Daniel Bridenbecker, Christopher Lorton, Jonathan Bloedow, Robert S. Baker, Guillaume Chabot‐Couture, Ye Chen, Thomas Fischle, Kurt Frey, Jillian Gauld, Hao Hu, Amanda S Izzo, Daniel J. Klein, Dejan Lukacevic, Kevin McCarthy, Joel C. Miller, André Lin Ouédraogo, T. Alex Perkins, Jeffrey Steinkraus, Quirine A. ten Bosch, Hung-Fu Ting, Svetlana Titova, Bradley G. Wagner, Philip A. Welkhoff, Edward A. Wenger, Christian N Wiswell

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ipyrad: Interactive assembly and analysis of RADseq datasets 由 Deren A. R. Eaton, Isaac Overcast

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Homology modeling in the time of collective and artificial intelligence 由 Tareq Hameduh, Yazan Haddad, Vojtěch Adam, Zbyněk Heger

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SpikeInterface, a unified framework for spike sorting 由 Alessio Paolo Buccino, Cole Hurwitz, Samuel Garcia, Jeremy F. Magland, Joshua H. Siegle, Roger Hurwitz, Matthias H. Hennig

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The <scp>ImageJ</scp> ecosystem: Open‐source software for image visualization, processing, and analysis 由 Alexandra B. Schroeder, Ellen T. A. Dobson, Curtis Rueden, Pavel Tomančák, Florian Jug, Kevin W. Eliceiri

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LocusZoom.js: interactive and embeddable visualization of genetic association study results 由 Andrew P. Boughton, Ryan Welch, Matthew Flickinger, Peter VandeHaar, Daniel Taliun, Gonçalo R. Abecasis, Michael Boehnke

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cellxgene: a performant, scalable exploration platform for high dimensional sparse matrices 由 Colin Megill, Bruce Martin, Charlotte A. Weaver, Sidney M. Bell, L.M. Prins, Seve Badajoz, Brian McCandless, Angela Oliveira Pisco, Marcus Kinsella, Fiona Griffin, Justin Kiggins, Genevieve Haliburton, Arathi Mani, Matthew Weiden, Madison I. Dunitz, Maximilian Lombardo, Timmy Huang, Trent M. Smith, Signe Chambers, Jeremy Freeman, Jonah Cool, Ambrose Carr

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Reproducible Analysis Pipeline for Data Streams: Open-Source Software to Process Data Collected With Mobile Devices 由 Julio Vega, Meng Li, Kwesi Aguillera, Nikunj Goel, Echhit Joshi, Kirtiraj Khandekar, Krina C Durica, Abhineeth Reddy Kunta, Carissa A. Low

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MMDetection: Open MMLab Detection Toolbox and Benchmark 由 Kai Chen, Jiaqi Wang, Jiangmiao Pang, Yuhang Cao, Yu Xiong, Xiaoxiao Li, Shuyang Sun, Wansen Feng, Ziwei Liu, Jiarui Xu, Zheng Zhang, Dazhi Cheng, Chenchen Zhu, Tianheng Cheng, Qijie Zhao, Buyu Li, Xin Lü, Rui Zhu, Yue Wu, Jifeng Dai, Jingdong Wang, Jianping Shi, Wanli Ouyang, Chen Change Loy, Dahua Lin

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YaHS: yet another Hi-C scaffolding tool 由 Chenxi Zhou, Shane McCarthy, Richard Durbin

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scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI 由 Haotian Cui, Xiaoming Wang, Hassaan Maan, Kuan Pang, Fengning Luo, Bo Wang

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ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction 由 Pascal Notin, Aaron W. Kollasch, Daniel P. Ritter, Lood van Niekerk, Steffan B. Paul, Hansen Spinner, Nathan Rollins, Ada Y. Shaw, Ruben Weitzman, Jonathan Frazer, Mafalda Dias, Dinko Franceschi, Rose Orenbuch, Yarin Gal, Debora S. Marks

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WashU Epigenome Browser update 2025 由 Chanrung Seng, Shane Liu, Wenjin Zhang, Xiaoyu Zhuo, Daofeng Li, Ting Wang

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